@article {pmid39657855,
year = {2024},
author = {Gu, Z and He, L and Liu, T and Xing, M and Feng, L and Luo, G},
title = {Exploring Strategies for Kitchen Waste Treatment and Remediation from the Perspectives of Microbial Ecology and Genomics.},
journal = {Chemosphere},
volume = {},
number = {},
pages = {143925},
doi = {10.1016/j.chemosphere.2024.143925},
pmid = {39657855},
issn = {1879-1298},
abstract = {Nowadays, the rapid growth of population has led to a substantial increase in kitchen waste and wasted sludge. Kitchen waste is rich in organic matter, including lignocellulose. Synergistic treatment involving kitchen waste and wasted sludge can enhance treatment process. Vermicomposting can facilitate microbial activities on organic matter. Nevertheless, the underlying mechanisms remain unclear. In this study, metagenomics was used to analyze microbial functional genes in vermicomposting. Redundancy analysis found that TOC, TN and DTN adversely affect earthworm growth and reproduction. The relative abundance of Bacteroidetes and Firmicutes were increased with earthworms, thereby potentially augmenting lignocellulose degradation. The predominant functional genes included amino acid, carbohydrate, and inorganic ion conversion and metabolism. Metagenomics analysis demonstrated that GH1, GH3, GH5, GH6, GH9, GH12, GH44, GH48 and GH74, GT41, GT4, GT2, and GT51 were dominant. Furthermore, there was higher abundance of carbohydrate-active enzymes in the vermicomposting, particularly during the later phases (30-45 days). Co-occurrence network revealed that Cellvibrio in the vermicomposting exhibited a relatively dense positive correlation with other microbial groups. The findings elucidated the mechanism of vermicomposting as a promising approach for managing kitchen waste and wasted sludge.},
}
@article {pmid39657789,
year = {2024},
author = {Zdouc, MM and Blin, K and Louwen, NLL and Navarro, J and Loureiro, C and Bader, CD and Bailey, CB and Barra, L and Booth, TJ and Bozhüyük, KAJ and Cediel-Becerra, JDD and Charlop-Powers, Z and Chevrette, MG and Chooi, YH and D'Agostino, PM and de Rond, T and Del Pup, E and Duncan, KR and Gu, W and Hanif, N and Helfrich, EJN and Jenner, M and Katsuyama, Y and Korenskaia, A and Krug, D and Libis, V and Lund, GA and Mantri, S and Morgan, KD and Owen, C and Phan, CS and Philmus, B and Reitz, ZL and Robinson, SL and Singh, KS and Teufel, R and Tong, Y and Tugizimana, F and Ulanova, D and Winter, JM and Aguilar, C and Akiyama, DY and Al-Salihi, SAA and Alanjary, M and Alberti, F and Aleti, G and Alharthi, SA and Rojo, MYA and Arishi, AA and Augustijn, HE and Avalon, NE and Avelar-Rivas, JA and Axt, KK and Barbieri, HB and Barbosa, JCJ and Barboza Segato, LG and Barrett, SE and Baunach, M and Beemelmanns, C and Beqaj, D and Berger, T and Bernaldo-Agüero, J and Bettenbühl, SM and Bielinski, VA and Biermann, F and Borges, RM and Borriss, R and Breitenbach, M and Bretscher, KM and Brigham, MW and Buedenbender, L and Bulcock, BW and Cano-Prieto, C and Capela, J and Carrion, VJ and Carter, RS and Castelo-Branco, R and Castro-Falcón, G and Chagas, FO and Charria-Girón, E and Chaudhri, AA and Chaudhry, V and Choi, H and Choi, Y and Choupannejad, R and Chromy, J and Donahey, MSC and Collemare, J and Connolly, JA and Creamer, KE and Crüsemann, M and Cruz, AA and Cumsille, A and Dallery, JF and Damas-Ramos, LC and Damiani, T and de Kruijff, M and Martín, BD and Sala, GD and Dillen, J and Doering, DT and Dommaraju, SR and Durusu, S and Egbert, S and Ellerhorst, M and Faussurier, B and Fetter, A and Feuermann, M and Fewer, DP and Foldi, J and Frediansyah, A and Garza, EA and Gavriilidou, A and Gentile, A and Gerke, J and Gerstmans, H and Gomez-Escribano, JP and González-Salazar, LA and Grayson, NE and Greco, C and Gomez, JEG and Guerra, S and Flores, SG and Gurevich, A and Gutiérrez-García, K and Hart, L and Haslinger, K and He, B and Hebra, T and Hemmann, JL and Hindra, H and Höing, L and Holland, DC and Holme, JE and Horch, T and Hrab, P and Hu, J and Huynh, TH and Hwang, JY and Iacovelli, R and Iftime, D and Iorio, M and Jayachandran, S and Jeong, E and Jing, J and Jung, JJ and Kakumu, Y and Kalkreuter, E and Kang, KB and Kang, S and Kim, W and Kim, GJ and Kim, H and Kim, HU and Klapper, M and Koetsier, RA and Kollten, C and Kovács, ÁT and Kriukova, Y and Kubach, N and Kunjapur, AM and Kushnareva, AK and Kust, A and Lamber, J and Larralde, M and Larsen, NJ and Launay, AP and Le, NT and Lebeer, S and Lee, BT and Lee, K and Lev, KL and Li, SM and Li, YX and Licona-Cassani, C and Lien, A and Liu, J and Lopez, JAV and Machushynets, NV and Macias, MI and Mahmud, T and Maleckis, M and Martinez-Martinez, AM and Mast, Y and Maximo, MF and McBride, CM and McLellan, RM and Bhatt, KM and Melkonian, C and Merrild, A and Metsä-Ketelä, M and Mitchell, DA and Müller, AV and Nguyen, GS and Nguyen, HT and Niedermeyer, THJ and O'Hare, JH and Ossowicki, A and Ostash, BO and Otani, H and Padva, L and Paliyal, S and Pan, X and Panghal, M and Parade, DS and Park, J and Parra, J and Rubio, MP and Pham, HT and Pidot, SJ and Piel, J and Pourmohsenin, B and Rakhmanov, M and Ramesh, S and Rasmussen, MH and Rego, A and Reher, R and Rice, AJ and Rigolet, A and Romero-Otero, A and Rosas-Becerra, LR and Rosiles, PY and Rutz, A and Ryu, B and Sahadeo, LA and Saldanha, M and Salvi, L and Sánchez-Carvajal, E and Santos-Medellin, C and Sbaraini, N and Schoellhorn, SM and Schumm, C and Sehnal, L and Selem, N and Shah, AD and Shishido, TK and Sieber, S and Silviani, V and Singh, G and Singh, H and Sokolova, N and Sonnenschein, EC and Sosio, M and Sowa, ST and Steffen, K and Stegmann, E and Streiff, AB and Strüder, A and Surup, F and Svenningsen, T and Sweeney, D and Szenei, J and Tagirdzhanov, A and Tan, B and Tarnowski, MJ and Terlouw, BR and Rey, T and Thome, NU and Torres Ortega, LR and Tørring, T and Trindade, M and Truman, AW and Tvilum, M and Udwary, DW and Ulbricht, C and Vader, L and van Wezel, GP and Walmsley, M and Warnasinghe, R and Weddeling, HG and Weir, ANM and Williams, K and Williams, SE and Witte, TE and Rocca, SMW and Yamada, K and Yang, D and Yang, D and Yu, J and Zhou, Z and Ziemert, N and Zimmer, L and Zimmermann, A and Zimmermann, C and van der Hooft, JJJ and Linington, RG and Weber, T and Medema, MH},
title = {MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae1115},
pmid = {39657789},
issn = {1362-4962},
support = {KICH1.LWV04.21.013//NWO/ ; 101000392//Horizon 2020/ ; OSF.23.1.044//NWO Open Science Project 'BiG-CODEC'/ ; 547394769//German Research Foundation/ ; //University of Sydney/ ; NNF22OC0078997//Novo Nodisk Foundation/ ; IM230100154//Australian Research Council Industry Fellowship/ ; //Hans Fischer Society/ ; //UK Government Department for Environment, Food & Rural Affairs (DEFRA) Global Centre on Biodiversity for the Climate/ ; EP/X03142X/1//United Kingdom Research and Innovation/ ; 101072485//Horizon Europe Marie Skłodowska-Curie/ ; //Indonesia Endowment Fund for Education Agency (LPDP)/ ; 106/IV/KS/11/2023//National Research and Innovation Agency/ ; 027/E5/PG.02.00.PL/2024//Ministry of Education/ ; MR/W011247/1//UKRI Future Leaders Fellowship/ ; 101117891-MeDiSyn//ERC Starting/ ; ANR-22-CE44-0011-01 UMISYN//Agence Nationale de la Recherche/ ; BB/X010953/1//Growing Health Institute Strategic Programme/ ; //Department of Biotechnology/ ; //National Agri-Food Biotechnology Institute/ ; 101087181//EU/ ; 212747/SNSF_/Swiss National Science Foundation/Switzerland ; 2021YFA0909500//National Key Research and Development Program of China/ ; 32170080//National Natural Science Foundation of China/ ; //Shanghai Pilot Program for Basic Research - Shanghai Jiao Tong University/ ; 21K06336//KAKENHI/ ; 21/07038-0//São Paulo Research Foundation/ ; VI.Veni.202.130//NWO Talent/ ; MR/V022334/1//UKRI Future Leaders Fellowship/ ; 222676//USDA Evans-Allen Research/ ; F32AT011475/AT/NCCIH NIH HHS/United States ; DGE 21-46756//National Science Foundation Graduate Research Fellowship/ ; //University of Illinois/ ; 802736//European Union Horizon 2020/ ; 735867//Consejo Nacional de Ciencia y Tecnología/ ; //NWO Merian/ ; BB/T007222/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 101066127//European Union/ ; RYC2020-029240-I//Ministerio de Ciencia, Innovación y Universidades/ ; K12 GM068524/GM/NIGMS NIH HHS/United States ; //HZI POF IV Cooperativity and Creativity Project Call/ ; //Alexander von Humboldt-Stiftung/ ; EXC-2124/1-09.029_0//Cluster of Excellence: Controlling Microbes to Fight Infection/ ; NRF-2020R1A6A1A03044512//Korean Government (MSIT)/ ; 2022R1C1C2004118//National Research Foundation of Korea/ ; NE/T010959/1//Signals in the Soil/ ; CZIF2022-007203//Chan Zuckerberg Initiative Foundation/ ; 495740318//German Research Foundation/ ; ANR-24-CE20-7299-01//Agence Nationale de la Recherche/ ; ANR-17-EUR-0007//EUR Saclay Plant Sciences-SPS/ ; 101072485//European Union's Horizon/ ; //European Regional Development Fund/ ; 802736//European Union's Horizon 2020/ ; EP/X03142X/1//United Kingdom Research and Innovation/ ; //Swiss Federal Government/ ; PS00349981//Fulbright/ ; 398967434-TRR 261//Deutsche Forschungsgemeinschaft/ ; DM60066//Italian Ministry of Research/ ; 1229222N//Research Foundation-Flanders (FWO)/ ; R01-GM146224/GM/NIGMS NIH HHS/United States ; NA22NOS4200050//NERRS/ ; BB/V005723/2//BBSRC/ ; 1347411//CONAHCYT/ ; T32GM136583/NH/NIH HHS/United States ; 101130799//European Union's Horizon/ ; CFB 2.0//Novo Nordisk Foundation/ ; //Basic Science Research Program/ ; NRF-RS-2024-00352229//Ministry of Science and ICT/ ; NRF 2018R1A5A2023127//Korea Government (MSIT)/ ; //Werner Siemens Foundation/ ; OCENW.XL21.XL21.088//NWO-XL/ ; DNRF137//Danish National Research Foundation/ ; NNF19SA0059360//Novo Nordisk Foundation INTERACT/ ; CBET-2032243//U.S. National Science Foundation/ ; //Delta Stewardship Council Delta Science Program/ ; //European Union's Horizon 2020 Research/ ; 852600//Innovation Program ERC St/ ; 101072485//European Union's Horizon Europe/ ; //Conahcyt Mexico International PhD Studentship/ ; //Strathclyde University Global Research Scholarship/ ; 3141-00013A//Innovation Fund Denmark/ ; K445/2022//Leibniz Association/ ; 23/01956-2//São Paulo Research Foundation/ ; DGE 2241144//NSF GRFP/ ; 024.004.014//MiCRop Consortium/ ; CF22-1239//Carlsberg Foundation/ ; 102022750//SINTEF/ ; 102029187//SEP AGREE/ ; 102024676-14//POS BIOINFO 2024/ ; 101106349//Marie Sklodowska-Curie/ ; 57/0009//Ministry of Education and Science of Ukraine/ ; //National Research Fund of Ukraine/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; //German Academic Scholarship Foundation/ ; OCENW.GROOT.2019.063//NWO-XL/ ; //Department of Biotechnology/ ; //University Grants Commission/ ; PROYEXCEL_00012//Spanish "Junta de Andalucía"/ ; GNT2021638//National Health and Medical Research Council/ ; DP230102668//Australian Research Council Discovery Project/ ; 101000794//SECRETed EU Project Horizon 2020/ ; 865738/ERC_/European Research Council/International ; T32-GM136629//Chemical-Biology Interface Training/ ; DGE 21-46756//National Science Foundation Graduate Research Fellowship/ ; 101055020-COMMUNITY//ERC Advanced/ ; 757173//Consejo Nacional de Ciencia y Tecnología/ ; //Horizon Europe Marie Skłodowska-Curie Actions Postdoctoral Fellowship/ ; 101099528//European Innovation Council/ ; 10062709//UK Innovation Funding Agency (UKRI)/ ; //Swedish Pharmaceutical Society PostDoc/ ; 205320_219638/SNSF_/Swiss National Science Foundation/Switzerland ; //Saarland University/ ; BB/X01097X/1//BBSRC Institute Strategic Program/ ; AUFF-E-2022-9-42//AUFF/ ; 101055020-COMMUNITY//ERC Advanced/ ; NNF22OC0079021//Novo Nordisk Foundation Postdoctoral Fellowship/ ; //Natural Science and Research Council of Canada/ ; TTU 09.826//German Center for Infection Research/ ; 10.55776/P 34036//Austrian Science Fund/ ; //Natural Sciences and Engineering Research Council of Canada Discovery/ ; DNRF137//Danish National Research Foundation CeMiSt/ ; },
abstract = {Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.},
}
@article {pmid39657562,
year = {2024},
author = {Du, Z and Du, Y and Wang, J and Zhang, Y and Lu, H and Zhang, F and Peng, Y},
title = {Acidophilic partial nitrification rapid startup and robustness validation for municipal wastewater treatment: Operation performance and microorganism insights.},
journal = {Water research},
volume = {272},
number = {},
pages = {122922},
doi = {10.1016/j.watres.2024.122922},
pmid = {39657562},
issn = {1879-2448},
abstract = {Acidophilic partial nitrification (a-PN) is a promising short-flow nitrogen conversion biotechnology, but achieving a rapid startup remains a significant challenge. This study explored strategies for starting up a-PN in real municipal wastewater treatment using sequencing batch reactors (SBRs). The influent alkalinity-to-NH4[+] molar ratio was maintained at 0.5-0.6 in the control reactor (SBRa), while other reactors were supplemented with sodium formate (150 mg COD/L, SBRb), hydroxylamine (5 mg/L, SBRc), and sludge alkaline fermentation liquid (NH4[+]-N=227.97±7.08 mg/L, COD=2463.98±125.17 mg/L, SBRd). Results indicated that the system using the composite strategy with sodium formate addition achieved a 93.7 % nitrite accumulation ratio (NAR) within just 4 days. Furthermore, stable a-PN performance was maintained in the systems without external substrate addition with pH ranging from 5.7 to 7.4. The established a-PN systems demonstrated robust performance, maintained a high NAR of 92.84 %-98.84 %, even under the intense impact of traditional nitrification biomass for 13 consecutive days. Although the relative abundances of Nitrosomonas and Nitrospira temporarily increased, traditional ammonia oxidizing bacteria and nitrite oxidizing bacteria were completely eliminated, falling to undetectable levels after long-term operation. Notably, amo and hao genes exhibited opposite trends: amo decreased significantly from 356 reads to 22-46 reads, while hao substantially increased by 186.6 %-613.1 %, from 626 reads to 1168-2838 reads. This suggests that hao may play a more crucial functional role in the a-PN process, and unidentified nitrifying communities may be driving acidophilic partial nitrification. Overall, our study advances the understanding of rapid startup strategies of a-PN and provides novel perspectives on the microbial structure and functional genes involved in a-PN system.},
}
@article {pmid39657473,
year = {2024},
author = {Hao, Y and Guo, T and Li, H and Liu, W and Chen, Z and Wang, X and Guo, J},
title = {Study on the mechanism of regulating micromolar Fe utilization and promoting denitrification by guanosine monophosphate (GMP) based multi-signal functional material Hematin@Fe/GMP.},
journal = {Journal of environmental management},
volume = {373},
number = {},
pages = {123610},
doi = {10.1016/j.jenvman.2024.123610},
pmid = {39657473},
issn = {1095-8630},
abstract = {A novel multi-signal functional material consisting of Hematin, Fe, and guanosine monophosphate (GMP) was successfully constructed (Hematin@Fe/GMP) to enhance denitrification efficiency based on the signal network regulation of electron transfer, micromolar Fe utilization, and microbial community. Hematin@Fe/GMP enhanced nitrate reduction rate by 2.33-fold with a 9.9 mg L[-1] h[-1] reduction rate. The mechanisms of accelerated denitrification were elaborated deeply from the electrochemical experiments, microbial metabolism activity, key enzyme activity, gene expression, and microbial community. Specifically, electrochemical experiments and X-ray photoelectron spectroscopy demonstrated that the released redox signal (Fe[2+]/Fe[3+]) promoted the increased redox substances (extracellular polymeric substances, cytochrome c, and riboflavin) to accelerate electron transfer efficiency. Metagenomic analysis suggested the released Fe utilization signal modulated siderophores genes (fhuB, fhuC, and fhuD) to promote the uptake and utilization of micromolar Fe, which was more conducive to synthesizing cytochrome c. Moreover, extracellular polymeric substances (EPS) stripping experiments demonstrated that the membrane-anchored cyt-c could shuttle in EPS and bind with Hematin@Fe/GMP to form an electrical conduit for accelerating denitrification efficiency. In inhibition experiments, Hematin@Fe/GMP could break down electron transfer barriers and restore/compensate for the electron transfer chain. Meanwhile, Hematin@Fe/GMP could restore the electrical signal disruption and synergize with the enriched signaling-capable microorganisms (Stutzerimonas and Thauera) to regulate quorum sensing. This research introduced multi-signal modulation of Hematin@Fe/GMP on denitrification and provided strategies for accelerating the biological transformation process and effectively utilizing micromolar Fe in practical applications.},
}
@article {pmid39657260,
year = {2024},
author = {Davis, JA and Chinthala, SP and Monty-Bromer, CN and Senko, JM},
title = {Electrochemical Detection of Carbon Steel Corrosion Induced by Fermentative Bacteria From Natural Gas Transmission Lines.},
journal = {Environmental microbiology reports},
volume = {16},
number = {6},
pages = {e70058},
doi = {10.1111/1758-2229.70058},
pmid = {39657260},
issn = {1758-2229},
support = {693JK31850003CAAP//Pipeline and Hazardous Materials Safety Administration/ ; },
mesh = {Corrosion ; *Steel/chemistry ; *Fermentation ; *Carbon/metabolism ; *Natural Gas/microbiology ; Bacteria/genetics/metabolism/classification/isolation & purification/growth & development ; Hydrogen-Ion Concentration ; Electrochemical Techniques/instrumentation ; Metagenome ; },
abstract = {The metabolic potential and corrosive activities of a fermentative bacterial enrichment culture from a natural gas transmission line were characterised. Three metagenome-assembled genomes (MAGs) attributable to Cytobacillus, Lacrimispora and Staphylococcus spp. were obtained. These MAGs hosted genes involved in the fermentation of carbohydrates to organic acids, which was reflected in the acidification of the growth medium by the culture. To evaluate the corrosive activities of the culture, it was incubated in a split chamber-zero resistance ammetry (SC-ZRA) format. This involved deploying carbon steel coupons immersed in liquid medium in opposing chambers of an electrochemical cell. Measurement of current between the coupons indicated the extent and mechanism of corrosion. When the enrichment culture was added to one side of an SC-ZRA incubation with bicarbonate-buffered medium, pH change and corrosion were minimal. In bicarbonate-free medium, the culture acidified the medium, induced electron transfer from the uninoculated chamber to the inoculated chamber, and caused mass loss. These results indicate that fermenter-induced microbially influenced corrosion (MIC) is due to localised fluid acidification, inducing anodic reactions on the metal surface exposed to the microorganisms and mass loss of the non-exposed metal.},
}
@article {pmid39656346,
year = {2024},
author = {Wu, H and Wang, Y and Yang, X and Lu, T and Luo, Y},
title = {Case report: diagnosis of neurobrucellosis in a non-endemic area child using metagenomic next-generation sequencing.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39656346},
issn = {1435-4373},
abstract = {Brucellosis with neurological symptoms at onset is rare in children and is frequently misdiagnosed or overlooked due to nonspecific clinical presentations, particularly in non-endemic areas. We report a case of neurobrucellosis in a child from a non-pastoral area, diagnosed via metagenomic next-generation sequencing (mNGS). The patient presented with headache and altered consciousness, accompanied by fever, projectile vomiting, seizures, and urinary incontinence. Physical examination indicated possible nuchal rigidity. Cerebrospinal fluid (CSF) analysis showed colorless and clear fluid, with a white blood cell count of 259 × 10[6]/L, 4.6% polymorphonuclear cells, positive protein qualitative test, protein level of 0.78 g/L, and glucose level of 1.66 mmol/L. Initial diagnosis suggested central nervous system infection, and empirical treatment led to improvement in consciousness. However, after a few days of stable body temperature, the patient experienced recurrent fever. Ultimately, mNGS of CSF identified Brucella melitensis, confirming neurobrucellosis. Following treatment with ceftriaxone, doxycycline, and rifampin, the patient's clinical symptoms improved significantly, and follow-up CSF analysis showed normalization of cell counts. This case highlights the early diagnostic utility of mNGS in CSF for neurobrucellosis and its role in differential diagnosis.},
}
@article {pmid39656004,
year = {2024},
author = {Jensen, EEB and Otani, S and Liachko, I and Auch, B and Aarestrup, FM},
title = {Using genomics to explore the epidemiology of vancomycin resistance in a sewage system.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0148924},
doi = {10.1128/spectrum.01489-24},
pmid = {39656004},
issn = {2165-0497},
abstract = {VanHAX-mediated glycopeptide resistance has been consistently high in one of the three main sewer systems in Copenhagen, Lynetten, for +20 years. To explore this for other glycopeptide resistance genes, and whether the colonization has resulted in establishment of multiple bacterial taxa, we mapped 505 shotgun metagenomic data sets from the inlet of three sewage treatment plants to 831 different glycopeptide resistance genes. Only vanHAX and vanHBX genes were differentially abundant in Lynetten. Analyses of eight contigs suggested limited variations in the flanking regions. Proximity ligation metagenomic analysis of 12 samples from Lynetten identified 441 and 5 paired reads mapping to vanHAX and vanHBX, respectively. The other end of these reads was mapped to generated metagenomic-assembled genomes and NCBI using BLAST. vanHBX could only be linked to the phylum level (Bacillota). Plasmid analysis of vanHBX Hi-C contigs showed that these were mainly located on plasmids reported found in enterococci species. Most vanHAX-linked reads could only be linked to phylum and class level, but some reads were assigned to Enterococcus faecium (7 reads), Enterococcus faecalis (4 reads), Paenibacillus apiarius (2 reads), and Paenibacillus thiaminolyticus (27 reads). Ten of the 20 Hi-C contigs-containing vanHAX were annotated as plasmid, all reported found in Enterococcus species. This study shows that while Hi-C technology is valuable for linking antimicrobial resistance genes to bacterial taxa, it suffers from challenges in reliably mapping the linked read to a genomic region with sufficient taxonomic information. Our results also suggest that over the +20 years of colonizing a sewer system, vanHAX has not become widespread across multiple taxa, remaining primarily in E. faecalis and E. faecium, with the exception of Paenibacillus.IMPORTANCELong-term colonization of microbial communities with antimicrobial-resistant bacteria is expected to result in sharing of the resistance genes between several different bacterial taxa of the communities. We investigated microbiomes from a sewer, which have been colonized with glycopeptide-resistant bacteria harboring the mobile vanHAX gene cluster for a minimum of 20 years, using metagenomics sequencing and Hi-C. We found that despite the long-term presence in the sewer, the vanHAX genes have seemingly not disseminated widely.},
}
@article {pmid39655960,
year = {2024},
author = {Tian, Q and Ye, H and Zhou, X and Wang, J and Zhang, L and Sun, W and Duan, C and Fan, M and Zhou, W and Bi, C and Ye, Q and Wong, A},
title = {Evaluating the health risk of probiotic supplements from the perspective of antimicrobial resistance.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0001924},
doi = {10.1128/spectrum.00019-24},
pmid = {39655960},
issn = {2165-0497},
abstract = {UNLABELLED: Antimicrobial resistance remains a public health threat. Probiotics harboring antimicrobial resistant genes (ARGs) have, in recent years, been considered a potential health risk. Studies conducted on probiotics from increasingly popular health supplements have raised the possibility of transmitting ARGs to commensals in the human gut, concomitantly establishing a reservoir of ARGs and risking acquisition by opportunistic pathogens. Building on our previous study that reported multiple antibiotic resistance in probiotics of health supplements, in this research, we have attempted to detect their ARGs that may account for resistant phenotypes. ARGs responsible for tetracycline, macrolide, aminoglycoside, and glycopeptide resistance were prevalent in probiotics. Through laboratory adaptive evolution studies, we also show that streptomycin-adapted probiotics gained resistance to erythromycin, tetracycline, and doxycycline more effectively than non-adapted ones. When co-incubated with Enterococcus faecalis, Escherichia coli, or Staphylococcus aureus on Caco-2 and/or HCT-116 cells, streptomycin resistance was transferred from the adapted probiotics to generate transconjugants at frequencies comparable to or higher than that of other studies conducted through filter mating. Consistently, ARGs conferring resistance to streptomycin (aadA) and erythromycin [erm(B)-1] were detected in E. coli and S. aureus transconjugants, respectively, after co-incubation with streptomycin-adapted probiotics on Caco-2 cells. aadA and erm(B)-1 were both detected in E. faecalis transconjugant after the same co-incubation on HCT-116 cells. Our data and future comparative genomics and metagenomics studies conducted on animal models and in healthy, immunocompromised, and/or antibiotic-treated human cohorts will contribute to a more comprehensive understanding of probiotic consumption, application, and safety.<br><br>IMPORTANCE: Probiotics are becoming increasingly popular, with promising applications in food and medicine, but the risk of transferring ARGs to disease-causing bacteria has raised concerns. Our study detected ARGs in probiotics of health supplements conferring resistance to tetracycline, macrolide, aminoglycoside, and glycopeptide drugs. Streptomycin-adapted probiotics also gained resistance to other antibiotics more effectively than non-adapted ones. Importantly, we showed that streptomycin resistance could be transferred to other bacteria after co-incubation with probiotics on human intestinal cells. ARGs responsible for erythromycin and streptomycin resistance, which were initially absent in the recipient bacteria, were also detected in the transconjugants. Our data build the foundation for future studies that will be conducted on animal models and in humans and leveraging advanced metagenomics approaches to clarify the long-term health risk of probiotic consumption.},
}
@article {pmid39655221,
year = {2024},
author = {Contreras-Peruyero, H and Nuñez, I and Vazquez-Rosas-Landa, M and Santana-Quinteros, D and Pashkov, A and Carranza-Barragán, ME and Perez-Estrada, R and Guerrero-Flores, S and Balanzario, E and Muñiz Sánchez, V and Nakamura, M and Ramírez-Ramírez, LL and Sélem-Mojica, N},
title = {CAMDA 2023: Finding patterns in urban microbiomes.},
journal = {Frontiers in genetics},
volume = {15},
number = {},
pages = {1449461},
pmid = {39655221},
issn = {1664-8021},
abstract = {The Critical Assessment of Massive Data Analysis (CAMDA) addresses the complexities of harnessing Big Data in life sciences by hosting annual competitions that inspire research groups to develop innovative solutions. In 2023, the Forensic Challenge focused on identifying the city of origin for 365 metagenomic samples collected from public transportation systems and identifying associations between bacterial distribution and other covariates. For microbiome classification, we incorporated both taxonomic and functional annotations as features. To identify the most informative Operational Taxonomic Units, we selected features by fitting negative binomial models. We then implemented supervised models conducting 5-fold cross-validation (CV) with a 4:1 training-to-validation ratio. After variable selection, which reduced the dataset to fewer than 300 OTUs, the Support Vector Classifier achieved the highest F1 score (0.96). When using functional features from MIFASER, the Neural Network model outperformed other models. When considering climatic and demographic variables of the cities, Dirichlet regression over Escherichia, Enterobacter, and Klebsiella bacteria abundances suggests that population increase is indeed associated with a rise in the mean of Escherichia while decreasing temperature is linked to higher proportions of Klebsiella. This study validates microbiome classification using taxonomic features and, to a lesser extent, functional features. It shows that demographic and climatic factors influence urban microbial distribution. A Docker container and a Conda environment are available at the repository: GitHub facilitating broader adoption and validation of these methods by the scientific community.},
}
@article {pmid39654977,
year = {2024},
author = {Wu, J and Wang, D and He, WJ and Li, JY and Mo, X and Li, YJ},
title = {Allergen-specific sublingual immunotherapy altered gut microbiota in patients with allergic rhinitis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1454333},
pmid = {39654977},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Sublingual Immunotherapy/methods ; *Rhinitis, Allergic/therapy/microbiology/immunology ; Male ; Female ; Adult ; *Feces/microbiology ; Allergens/immunology ; Young Adult ; Animals ; Middle Aged ; Antigens, Dermatophagoides/immunology ; Dermatophagoides farinae/immunology ; Treatment Outcome ; Adolescent ; Metagenomics/methods ; },
abstract = {INTRODUCTION: Allergen-specific immunotherapy (AIT) induces long-term immune tolerance to allergens and is effective for treating allergic rhinitis (AR). However, the impact of sublingual immunotherapy (SLIT) on gut microbiota from AR patients and its correlation with treatment efficacy remains unclear.<br><br>METHODS: In the present study, we enrolled 24 AR patients sensitized to Dermatophagoides farinae (Der-f) and 6 healthy donors (HD). All AR patients received SLIT treatment using standardized Der-f drops. Stool samples were collected from AR patients before treatment, and 1- and 3-months post-treatment, as well as from HD, for metagenomic sequencing analysis.<br><br>RESULTS: AR patients had significantly lower richness and diversity in gut microbiota compared to HD, with notable alterations in composition and function. Besides, three months post-SLIT treatment, significant changes in gut microbiota composition at the genus and species levels were observed in AR patients. Streptococcus parasanguinis_B and Streptococcus parasanguinis, which were significantly lower in AR patients compared to HD, increased notably after three months of treatment. LEfSe analysis identified these species as markers distinguishing HD from AR patients and AR patients pre- from post-SLIT treatment. Furthermore, changes in the relative abundance of S. parasanguinis_B were negatively correlated with changes in VAS scores but positively correlated with changes in RCAT scores, suggesting a positive correlation with effective SLIT treatment.<br><br>DISCUSSION: SLIT treatment significantly alters the gut microbiota of AR patients, with S. parasanguinis_B potentially linked to its effectiveness. This study offers insights into SLIT mechanisms and suggests that specific strains may serve as biomarkers for predicting SLIT efficacy and as modulators for improving SLIT efficacy.},
}
@article {pmid39654975,
year = {2024},
author = {Jarmukhanov, Z and Mukhanbetzhanov, N and Vinogradova, E and Kozhakhmetov, S and Kushugulova, A},
title = {Gut metagenomic features of frailty.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1486579},
pmid = {39654975},
issn = {2235-2988},
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Frailty/microbiology/metabolism ; Male ; Female ; Aged ; Middle Aged ; *Feces/microbiology ; *Metagenomics/methods ; Kazakhstan ; Adult ; Metagenome ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Aged, 80 and over ; Metabolic Networks and Pathways/genetics ; },
abstract = {This study investigates the relationship between frailty severity and gut microbiome characteristics in adults in Kazakhstan. We analyzed 158 participants across four frailty severity (mild to very severe) using metagenomic sequencing of stool samples. Frailty was significantly correlated with age, weight, and functional measures like walking speed and grip strength. Microbial diversity decreased significantly with increasing frailty. Beta diversity analysis revealed distinct clustering patterns based at phylum level. Taxonomically, we observed a significant inverse correlation between Firmicutes abundance and frailty. Classes like Clostridia and Erysipelotrichia decreased with frailty, while Bacteroidia and Actinobacteria increased. At the family level, Oscillospiraceae showed a positive correlation with frailty. Functionally, we identified significant correlations between frailty measures and specific metabolic pathways. The frailty index negatively correlated with pathways involved in cobalamin, arginine and molybdenum cofactor biosynthesis and positively correlated with folate biosynthesis. Physical performance measures strongly correlated with pathways related to nucleotide biosynthesis, and one-carbon metabolism. We propose these identified features may constitute a "frailty-associated metabolic signature" in the gut microbiome. This signature suggests multiple interconnected mechanisms through which the microbiome may influence frailty development, including modulation of inflammation, alterations in energy metabolism, and potential impacts on muscle function through microbial metabolites.},
}
@article {pmid39654973,
year = {2024},
author = {Ding, H and Huang, J and Lin, L and Chen, Y and Wang, Q and Li, W and Huang, Y and Fang, X and Zhang, W},
title = {Shedding light on negative cultures in osteoarticular infections: leveraging mNGS to unravel risk factors and microbial profiles.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1457639},
pmid = {39654973},
issn = {2235-2988},
mesh = {Humans ; Female ; Risk Factors ; Male ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; Child, Preschool ; Anti-Bacterial Agents/therapeutic use ; Child ; Osteomyelitis/microbiology/diagnosis ; Middle Aged ; Bacteria/genetics/classification/isolation &amp; purification ; Infant ; Adult ; Adolescent ; Aged ; },
abstract = {BACKGROUND: The objective of this study is to utilize metagenomic next-generation sequencing (mNGS) to analyze the risk factors causing negative microbial cultures, comprehensively delineate the microbial profiles neglected by traditional cultures, and optimize the pathogenetic diagnostic procedure accordingly.<br><br>RESEARCH DESIGN AND METHODS: We enrolled 341 patients diagnosed with OI at our center between 2016 and 2022, and gathered data including age, gender, clinical diagnosis, duration of antibiotic use prior to sampling, microbial culture results, and mNGS results for these patients. According to microbial detection results, risk factors for negative microbial culture and mNGS results were investigated through univariate and multivariate analyses, and the microbial profile in cases with negative microbial cultures was summarized in conjunction with mNGS results. Building upon this, we suggest strategies to enhance the positivity rate of microbial cultures based on clinical experience.<br><br>RESULTS: Invasive osteoarticular infection (IOI), multi-infections, rare pathogen infections, and prior antibiotic use are risk factors for negative microbial cultures. When the duration of prior antibiotic use is &#x2265;3 days, mNGS demonstrates significantly higher pathogen detection efficiency than microbial culture. Moreover, the risk of negative microbial culture increases by 4.8 times with the exposure to each additional risk factor (OR=4.043, 95%CI [2.835, 5.765], P<0.001). Additionally, over one-third of culture-negative OI involve polymicrobial infections or rare pathogens.<br><br>CONCLUSIONS: Clinicians should tailor microbial culture strategies based on patient conditions. When needed, they can collaborate with mNGS or optimize microbial culture conditions based on mNGS results to enhance the efficiency of pathogen diagnosis.},
}
@article {pmid39654219,
year = {2024},
author = {Wang, R and Lv, M and Fu, L and Zhao, J and Ni, Y and Li, T and Chen, Z and Li, F},
title = {A rare case report of infective endocarditis caused by Enterococcus gallinarum following renal laser lithotripsy.},
journal = {Medicine},
volume = {103},
number = {49},
pages = {e40802},
doi = {10.1097/MD.0000000000040802},
pmid = {39654219},
issn = {1536-5964},
support = {To Wang, Ruoxin MD, Ph.D.//the Scientific Research Grant of Shanghai Jiao Tong University Affiliated Sixth People's Hospital Medical Group/ ; },
mesh = {Humans ; Male ; Middle Aged ; *Enterococcus/isolation &amp; purification ; *Anti-Bacterial Agents/therapeutic use ; *Endocarditis, Bacterial/microbiology/diagnosis/drug therapy ; Gram-Positive Bacterial Infections/diagnosis/microbiology ; Lithotripsy/adverse effects ; Heart Valve Prosthesis Implantation/adverse effects ; Daptomycin/therapeutic use ; },
abstract = {RATIONALE: Enterococcus gallinarum is a part of the normal fecal microbiota in the general population and animals, and is rarely isolated in clinical specimens. Due to the increasing use of immunosuppressants, invasive treatments, and overuse of antibiotics, infections caused by enterococci are gradually increasing.<br><br>PATIENT CONCERNS: A 48-year-old man was admitted to our hospital due to a persistent fever for 1 month after renal laser lithotripsy.<br><br>DIAGNOSES: The cardiac ultrasound showed a mass on the mitral valve leaflet of the left atrium. The metagenomic next-generation sequencing test results of blood and vegetation were positive, reporting a large number of characteristic reads of E. gallinarum. The patient was diagnosed with infective endocarditis.<br><br>INTERVENTIONS: Mechanical mitral valve replacement was performed, and daptomycin was administered during the perioperative period.<br><br>OUTCOMES: After 4 weeks of antibiotic treatment, the patient's inflammatory indexes were normal, and no abnormalities such as fever were found. Blood culture and metagenomic next-generation sequencing test results were negative. The patient was then discharged from the hospital.<br><br>LESSONS: This case emphasizes the possibility of E. gallinarum developing severe invasive infections after kidney surgery. Clinical doctors should strengthen their understanding of this type of bacteria, understand their sensitive characteristics and treatment principles.},
}
@article {pmid39653697,
year = {2024},
author = {Palladino, G and Nanetti, E and Scicchitano, D and Cinti, N and Foresto, L and Cozzi, A and Gonzalez Vara Rodriguez, A and Interino, N and Fiori, J and Turroni, S and Candela, M and Rampelli, S},
title = {Zonation of the Vitis vinifera microbiome in Vino Nobile di Montepulciano PDO production area.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1626},
pmid = {39653697},
issn = {2399-3642},
support = {818290//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
mesh = {*Vitis/microbiology ; *Microbiota/genetics ; Italy ; *Wine/microbiology ; Soil Microbiology ; Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Fungi/genetics/classification/metabolism ; Rhizosphere ; },
abstract = {The microbial dimension of the terroir is crucial for wine quality, as microbiomes contribute to plant biofertilization, stress tolerance and pathogen suppression. While microbial terroir can act as a biological signature at large scale, data for local contexts is lacking, hindering the characterization of regional microbial diversity in vineyards. Here, we define the microbial terroir of vineyards across the 12 sub-areas (Additional Geographic Units -AGUs) of the "Consorzio del Vino Nobile di Montepulciano DOCG" PDO area (Italy), a world-renowned wine-producing region. Rhizospheres of Vitis vinifera cultivar Sangiovese and soil samples were collected throughout the 2022 viticultural season and analyzed through an integrated metabarcoding/shotgun metagenomic approach, targeting bacteria and fungi. Wine metabolomics was also perfomed, projecting compositional and functional variations of the microbial terroir at the AGUs level into a corresponding variation in the product metabolic profile. Our findings reveal a unique taxonomic configuration of the Vino Nobile di Montepulciano terroir compared to other vineyards, with microbiomes being "AGU-specific" in taxonomic abundances and plant growth-promoting functions, confirming the potential relevance of characterizing and preserving the microbial terroir to safeguard high-quality traditional wines.},
}
@article {pmid39653684,
year = {2024},
author = {Chen, Y and Yang, C and Deng, Z and Xiang, T and Tan, J and Xu, J and Sun, D and Luo, F},
title = {Alterations of gut virome with close interaction in the progression of estrogen deficiency-induced osteoporosis.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2437250},
doi = {10.1080/19490976.2024.2437250},
pmid = {39653684},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome ; Animals ; Female ; *Virome ; Mice ; *Osteoporosis/virology ; Humans ; *Estrogens/metabolism ; Ovariectomy ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Mice, Inbred C57BL ; Disease Models, Animal ; Disease Progression ; },
abstract = {Previous research has established a link between gut microbiota and osteoporosis (OP) advancement. However, there remains a limited understanding of the crucial contribution of the gut virome in the onset and progression of OP. We employed metagenomic shotgun sequencing and gut virome sequencing to process the ovariectomy (OVX)-induced OP murine model, which revealed significant disparities in bacteriome and virome compositions between subjects with OP and healthy controls. One hundred and seventy-four altered viral strains were identified to participate in the multifaceted regulation of bone loss, involving immune modulation, microbial metabolic activity, and intricate host-virus dynamics. Our findings suggested that the gut virome may influence bone metabolism, potentially altering the balance of bone-modulating compounds like short-chain fatty acids. This comprehensive analysis of the gut virome in OP highlighted the diagnostic potential of combined gut viral and bacterial biomarkers for OP.},
}
@article {pmid39653637,
year = {2024},
author = {Lepcha, A and Kumar, R and Dindhoria, K and Bhargava, B and Pati, AM and Kumar, R},
title = {Metagenomic insights into the functional potential of non-sanitary landfill microbiomes in the Indian Himalayan region, highlighting key plastic degrading genes.},
journal = {Journal of hazardous materials},
volume = {484},
number = {},
pages = {136642},
doi = {10.1016/j.jhazmat.2024.136642},
pmid = {39653637},
issn = {1873-3336},
abstract = {Solid waste management in the Indian Himalayan Region (IHR) is a growing challenge, intensified by increasing population and tourism, which strain non-sanitary landfills. This study investigates microbial diversity and functional capabilities within these landfills using a high-throughput shotgun metagenomic approach. Physicochemical analysis revealed that the Manali and Mandi landfill sites were under heavy metal contamination and thermal stress. Taxonomic annotation identified a dominance of bacterial phyla, including Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes, with genera like Pseudomonas and Bacillus prevalent. Squeezemeta analysis generated 9,216,983 open reading frames (ORFs) across the sampling sites, highlighting diverse metabolic potentials for heavy metal resistance and degrading organic, xenobiotics and plastic wastes. Hierarchical clustering and principal component analysis (PCA) identified distinct gene clusters in Manali and Mandi landfill sites, reflecting differences in pollution profiles. Functional redundancy of landfill microbiome was observed with notable xenobiotic and plastic degradation pathways. This is the first comprehensive metagenomic assessment of non-sanitary landfills in the IHR, providing valuable insights into the microbial roles in degrading persistent pollutants, plastic waste, and other contaminants in these stressed environments.},
}
@article {pmid39653411,
year = {2024},
author = {Shi, Z and Li, M and Zhang, C and Li, H and Zhang, Y and Zhang, L and Li, X and Li, L and Wang, X and Fu, X and Sun, Z and Zhang, X and Tian, L and Zhang, M and Chen, WH and Li, Z},
title = {Butyrate-producing Faecalibacterium prausnitzii suppresses natural killer/T-cell lymphoma by dampening the JAK-STAT pathway.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2024-333530},
pmid = {39653411},
issn = {1468-3288},
abstract = {BACKGROUND: Natural killer/T-cell lymphoma (NKTCL) is a highly aggressive malignancy with a dismal prognosis, and gaps remain in understanding the determinants influencing disease outcomes.<br><br>OBJECTIVE: To characterise the gut microbiota feature and identify potential probiotics that could ameliorate the development of NKTCL.<br><br>DESIGN: This cross-sectional study employed shotgun metagenomic sequencing to profile the gut microbiota in two Chinese NKTCL cohorts, with validation conducted in an independent Korean cohort. Univariable and multivariable Cox proportional hazards analyses were applied to assess associations between identified marker species and patient outcomes. Tumour-suppressing effects were investigated using comprehensive in vivo and in vitro models. In addition, metabolomics, RNA sequencing, chromatin immunoprecipitation sequencing, Western blot analysis, immunohistochemistry and lentiviral-mediated gene knockdown system were used to elucidate the underlying mechanisms.<br><br>RESULTS: We first unveiled significant gut microbiota dysbiosis in NKTCL patients, prominently marked by a notable reduction in Faecalibacterium prausnitzii which correlated strongly with shorter survival among patients. Subsequently, we substantiated the antitumour properties of F. prausnitzii in NKTCL mouse models. Furthermore, F. prausnitzii culture supernatant demonstrated significant efficacy in inhibiting NKTCL cell growth. Metabolomics analysis revealed butyrate as a critical metabolite underlying these tumour-suppressing effects, validated in three human NKTCL cell lines and multiple tumour-bearing mouse models. Mechanistically, butyrate suppressed the activation of Janus kinase-signal transducer and activator of transcription pathway through enhancing histone acetylation, promoting the expression of suppressor of cytokine signalling 1.<br><br>CONCLUSION: These findings uncover a distinctive gut microbiota profile in NKTCL and provide a novel perspective on leveraging the therapeutic potential of F. prausnitzii to ameliorate this malignancy.},
}
@article {pmid39652203,
year = {2024},
author = {Thillapudi, J and Mendonce, KC and Palani, N and Bhowmik, S and Rajadesingu, S},
title = {Revealing the nutritious treasures: an extensive investigation of health benefits of cultured dairy foods.},
journal = {Archives of microbiology},
volume = {207},
number = {1},
pages = {12},
pmid = {39652203},
issn = {1432-072X},
mesh = {Humans ; *Cultured Milk Products/microbiology ; Functional Food ; Animals ; Lactobacillales/genetics/metabolism ; Dairy Products/microbiology ; },
abstract = {Cultured milk products including yogurt, buttermilk, and lassi have made their way into South Asian cuisine for hundreds of years and are extraordinarily beneficial to human health. With a study background on lactic acid bacteria (LAB), these products are scientifically proved to aid in strengthening the immune system, for their anti-mutagenic effects, suitability for those who are lactose intolerant, and for protection against cancer, osteoporosis, and gut disorders. As of now, no scientific attention has been given to the microbial diversity of cultured milk products despite its prominent production and importance in the culture. New emerging approaches for studying the genetic composition and metabolic features of microbial communities, such as metagenomics and metabolomics, will open up important sources of knowledge and be a significant tool for informing conservation. These products are highly valued worldwide in the management of cardiometabolic diseases (CMDs), which encompass hypertension, type 2 diabetes, and obesity. The aim of this article will therefore advocate for the health benefits as well as cultural importance of cultured milk products. Indian fermented milk products, along with their historical development, cultural, and research aspects, thereby, highlighting the potential of this kind of product in promoting global health through functional food application, with a focus on recent advancements in their therapeutic potential and applications.},
}
@article {pmid39651889,
year = {2024},
author = {Wang, J and Schamp, CN and Hudson, LK and Chaggar, HK and Bryan, DW and Garman, KN and Radosevich, M and Denes, TG},
title = {Whole-genome sequencing and metagenomics reveal diversity and prevalence of Listeria spp. from soil in the Nantahala National Forest.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0171224},
doi = {10.1128/spectrum.01712-24},
pmid = {39651889},
issn = {2165-0497},
abstract = {UNLABELLED: Listeria spp. are widely distributed environmental bacteria associated with human foodborne illness. The ability to detect and characterize Listeria strains in the natural environment will contribute to improved understanding of transmission routes of contamination. The current standard for surveillance and outbreak source attribution is whole-genome sequencing (WGS) of Listeria monocytogenes clinical isolates. Recently, metagenomic sequencing has also been explored as a tool for the detection of Listeria spp. in environmental samples. This study evaluated soil samples from four locations across altitudes ranging from 1,500 to 4,500 ft in the Nantahala National Forest in North Carolina, USA. Forty-two Listeria isolates were cultured and sequenced, and 12 metagenomes of soil bacterial communities were generated. These isolates comprised 14 distinct strains from five species, including Listeria cossartiae subsp. cayugensis (n = 8; n represents the number of distinct strains), L. monocytogenes (n = 3), "Listeria swaminathanii" (Lsw) (n = 1), Listeria marthii (n = 1), and Listeria booriae (n = 1). Most strains (n = 13) were isolated from lower altitudes (1,500 or 2,500 ft), while the L. swaminathanii strain was isolated from both higher (4,500 ft) and lower (1,500 ft) altitudes. Metagenomic analysis of soil described a reduction in both bacterial community diversity and relative abundance of Listeria spp. as the altitude increased. Soil pH and cation exchange capacity were positively correlated (P < 0.05) with the abundance of Listeria spp. as detected by metagenomics. By integrating culture-independent metagenomics with culture-based WGS, this study advances current knowledge regarding distribution of Listeria spp. in the natural environment and suggests the potential for future use of culture-independent methods in tracking the transmission of foodborne pathogens.<br><br>IMPORTANCE: As a foodborne pathogen, Listeria continues to cause numerous illnesses in humans and animals. Studying the diversity and distribution of Listeria in soil is crucial for understanding potential sources of contamination and developing effective strategies to prevent foodborne outbreaks of listeriosis. Additionally, examining the ecological niches and survival mechanisms of Listeria in natural habitats provides insights into its persistence and adaptability, informing risk assessments and public health interventions. This research contributes to a broader understanding of microbial ecology and the factors influencing foodborne pathogen emergence, ultimately enhancing food safety and protecting public health. Moreover, using a metagenomic approach provides a detailed understanding of the soil microbial ecosystems, leading to more effective monitoring and control of foodborne pathogens. This study also highlights the potential for integrating metagenomics into routine surveillance systems for food safety in the near future.},
}
@article {pmid39651865,
year = {2024},
author = {Howland, KE and Mouradian, JJ and Uzarski, DR and Henson, MW and Uzarski, DG and Learman, DR},
title = {Nutrient amendments enrich microbial hydrocarbon degradation metagenomic potential in freshwater coastal wetland microcosm experiments.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0197224},
doi = {10.1128/aem.01972-24},
pmid = {39651865},
issn = {1098-5336},
abstract = {UNLABELLED: Biostimulating native microbes with fertilizers has proven to be a highly effective strategy to speed up biodegradation rates in microbial communities. This study investigates the genetic potential of microbes to degrade light synthetic crude oil in a freshwater coastal wetland. Experimental sediment microcosms were exposed to a variety of conditions (biological control, a light synthetic crude oil amendment, and light synthetic crude oil with nutrient amendment) and incubated for 30 days before volatile organic compounds (BTEX) were quantified and DNA was sequenced for metagenomic analysis. The resulting DNA sequences were binned into metagenome-assembled genomes (MAGs). Analyses of MAGs uncovered a 13-fold significant increase in the abundance of rate-limiting hydrocarbon degrading monooxygenases and dioxygenases, identified only in MAGs from the light synthetic crude oil with nutrient amendments. Further, complete degradation pathways for BTEX compounds were found only in MAGs resulting from the light synthetic crude with nutrient amendment. Moreover, volatile organic compounds (BTEX, cyclohexane, and naphthalene) analyses of microcosm sediments in the presence of nutrients documented that benzene was degraded below detection limits, toluene (98%) and ethylbenzene (67%) were predominantly reduced within 30 days. Results indicate that the genetic potential to degrade BTEX compounds in this freshwater wetland can be linked to the functional potential for bioremediation. BTEX compounds are typically more recalcitrant and tougher to degrade than alkanes. This study demonstrated that stimulating a microbial community with nutrients to enhance its ability to biodegrade hydrocarbons, even in a relatively nutrient-rich habitat like a freshwater wetland, is an effective remediation tactic.<br><br>IMPORTANCE: The impact of oil spills in a freshwater aquatic environment can pose dire social, economic, and ecological effects on the region. An oil spill in the Laurentian Great Lakes region has the potential to affect the drinking water of more than 30 million people. The light synthetic crude oil used in this experimental microcosm study is transported through an underground pipeline crossing the waterway between two Laurentian Great Lakes. This study collected metagenomic data (experiments in triplicate) and assessed the quantity of BTEX compounds, which connected microbial degradation function to gene potential. The resulting data documented the bioremediation capabilities of native microbes in a freshwater coastal wetland. This study also provided evidence for this region that bioremediation can be a viable remediation strategy instead of invasive physical methods.},
}
@article {pmid39650650,
year = {2024},
author = {Xue, Y and Mo, J and Cheng, K and Xue, Y and Chen, D and Lin, F and Chen, H},
title = {Case report: Unveiling the silent threat in the ICU - a case of disseminated invasive aspergillosis in a patient with fulminant myocarditis.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1481335},
doi = {10.3389/fimmu.2024.1481335},
pmid = {39650650},
issn = {1664-3224},
mesh = {Humans ; Female ; Adult ; *Myocarditis/diagnosis/etiology/therapy ; *Intensive Care Units ; Antifungal Agents/therapeutic use ; Invasive Pulmonary Aspergillosis/diagnosis/etiology ; Extracorporeal Membrane Oxygenation ; Aspergillosis/diagnosis/drug therapy ; Immunocompromised Host ; Positron Emission Tomography Computed Tomography ; },
abstract = {Invasive aspergillosis (IA) significantly increases mortality in critically ill patients in the ICU and its occurrence is closely related to immunocompromise. Dissemination of IA is easily misdiagnosed and mistreated due to its ability to invade multiple systems throughout the body and lack of typical clinical manifestations. In this case, a 25-year-old previously healthy woman was hospitalized with fulminant myocarditis and treated with veno-arterial extracorporeal membrane pulmonary oxygenation (VA-ECMO) support and intravenous acyclovir, high-dose methylprednisolone, and immunoglobulin. 6 days later, she was successfully weaned from VA-ECMO and underwent cardiac rehabilitation. On day 10, she developed a fever (Tmax 38.3°C) and an irritating cough and began to experience reduced vision over the right eye with eye pain, redness, photophobia, and tearing 2 days later. Administration of levofloxacin eye drops and tobramycin/dexamethasone eye ointment was ineffective. The patient was positive for serum Aspergillus galactomannan antigen. Positron emission tomography/computed tomography (PET/CT) scan showed multiple hypermetabolic cavitary nodules in both lungs (SUVmax3.6) and thickening of the ocular ring wall with hypermetabolism in the right eye (SUVmax3.2). Ophthalmologic examination revealed that her best-corrected visual acuity in the right eye was reduced to light perception with an intraocular pressure of 21 mmHg, and B-scan ultrasonography showed vitreous opacity and retinal edema with mild detachment in the right eye. Metagenomic next-generation sequencing (mNGS) identified a large number of Aspergillus fumigatus sequences in bronchoalveolar lavage fluid, blood, and aqueous humor from the right eye, supporting the diagnosis of pulmonary and ocular involvement due to disseminated IA. Vitrectomy, anterior chamber irrigation, combined with intravenous and intravitreal injections of voriconazole and liposomal amphotericin B eventually cured the patient. This case highlights the importance of early identification and intervention regarding disseminated IA in immunocompromised critically ill patients, especially in the presence of multiple organ involvement.},
}
@article {pmid39650139,
year = {2024},
author = {Liu, Y and Ghaffari, MH and Ma, T and Tu, Y},
title = {Impact of database choice and confidence score on the performance of taxonomic classification using Kraken2.},
journal = {aBIOTECH},
volume = {5},
number = {4},
pages = {465-475},
doi = {10.1007/s42994-024-00178-0},
pmid = {39650139},
issn = {2662-1738},
abstract = {UNLABELLED: Accurate taxonomic classification is essential to understanding microbial diversity and function through metagenomic sequencing. However, this task is complicated by the vast variety of microbial genomes and the computational limitations of bioinformatics tools. The aim of this study was to evaluate the impact of reference database selection and confidence score (CS) settings on the performance of Kraken2, a widely used k-mer-based metagenomic classifier. In this study, we generated simulated metagenomic datasets to systematically evaluate how the choice of reference databases, from the compact Minikraken v1 to the expansive nt- and GTDB r202, and different CS (from 0 to 1.0) affect the key performance metrics of Kraken2. These metrics include classification rate, precision, recall, F1 score, and accuracy of true versus calculated bacterial abundance estimation. Our results show that higher CS, which increases the rigor of taxonomic classification by requiring greater k-mer agreement, generally decreases the classification rate. This effect is particularly pronounced for smaller databases such as Minikraken and Standard-16, where no reads could be classified when the CS was above 0.4. In contrast, for larger databases such as Standard, nt and GTDB r202, precision and F1 scores improved significantly with increasing CS, highlighting their robustness to stringent conditions. Recovery rates were mostly stable, indicating consistent detection of species under different CS settings. Crucially, the results show that a comprehensive reference database combined with a moderate CS (0.2 or 0.4) significantly improves classification accuracy and sensitivity. This finding underscores the need for careful selection of database and CS parameters tailored to specific scientific questions and available computational resources to optimize the results of metagenomic analyses.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42994-024-00178-0.},
}
@article {pmid39650020,
year = {2024},
author = {Vermeersch, AS and Van Nieuwerburgh, F and Gansemans, Y and Ali, M and Ducatelle, R and Geldhof, P and Deforce, D and Callens, J and Opsomer, G},
title = {Multi-omics analysis elucidates the host-microbiome interplay in severe udder cleft dermatitis lesions in dairy cows.},
journal = {JDS communications},
volume = {5},
number = {6},
pages = {598-601},
doi = {10.3168/jdsc.2023-0537},
pmid = {39650020},
issn = {2666-9102},
abstract = {Udder cleft dermatitis is a skin disease in dairy cattle that is characterized by painful, large open wounds between the udder halves or at the front udder attachment. Its impact on animal welfare and production warrants an in-depth investigation of its pathogenesis. The present study delves into the pathophysiology of severe udder cleft dermatitis, employing a multi-omics approach by integrating transcriptomic and metagenomic data obtained from samples of severe udder cleft dermatitis lesions and healthy udder skin of dairy cattle. All dominant features selected from the virulence factor, taxonomic, and transcriptomic datasets, except for the facultative pathogen Streptococcus pyogenes, form a network that could be associated with the healthy udder skin. The severe udder cleft dermatitis-associated Streptococcus pyogenes exhibited a negative correlation with these virulence factors and genes, but was not correlated with the other commensal bacteria in the analysis. Examining the different components interacting with each other could advance our understanding of the pathogenesis of severe udder cleft dermatitis.},
}
@article {pmid39648978,
year = {2024},
author = {Ribero, MN and Schiaffino, MR and Filloy, J},
title = {Grassland Afforestation Drives Biotic Homogenisation of Soil Microbial Communities at a Regional Scale.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17617},
doi = {10.1111/mec.17617},
pmid = {39648978},
issn = {1365-294X},
support = {2018//Secretar&#xed;a de Ciencia y T&#xe9;cnica, Universidad de Buenos Aires/ ; //Neotropical Grassland Conservancy/ ; PICT 2017//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; //Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas/ ; },
abstract = {Grassland afforestation poses a threat to biodiversity beyond land-use conversion. Diversity patterns are shaped by temporal dynamics, particularly, time since afforestation can decline beta diversity and lead to biotic homogenisation. Our study examines the effect of grassland afforestation on soil prokaryotic and fungal beta diversity. We evaluate the contributions of colonisation and extinction processes to beta diversity, as well as the replacement of endemic species by ubiquitous ones. Along a 200 km climatic gradient in Argentina's Pampas region, we analysed grasslands and mature eucalypt plantations at different times since afforestation. Soil samples were collected at each site and analysed using 16S (V3-V4) and ITS2 amplicon sequencing to identify prokaryotic and fungal communities, respectively. The analyses revealed biotic homogenisation at the transition from grassland to newly planted stands, evidenced by a decrease in intratreatment beta diversity. Increasing time since afforestation did not exacerbate this decline. However, our findings indicate that there are different responses between prokaryotes and fungi. The homogenisation of prokaryotes in young stands is due to the low heterogeneity in colonising communities. On the other hand, the decline in fungal beta diversity is likely caused by other mechanisms beyond extinction or replacement. The study highlights the impacts of the afforestation process on the beta diversity of soil microbial communities of grasslands, affecting taxonomic groups in different ways. Although microbial diversity may be partially restored in time in eucalypt plantations, it is important to investigate its underlying mechanisms and the ecological implications for microbial diversity and its spatial distribution.},
}
@article {pmid39647771,
year = {2024},
author = {Chen, R and Xu, R and Huang, J and Zhu, X and Tang, Y and Zhang, Y},
title = {N-acyl-homoserine-lactones as a critical factor for biofilm formation during the initial adhesion stage in drinking water distribution systems.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125489},
doi = {10.1016/j.envpol.2024.125489},
pmid = {39647771},
issn = {1873-6424},
abstract = {The N-acyl-homoserine-lactone (AHLs)-mediated quorum sensing (QS) system is crucial for the coordination of microbial behaviors within communities. However, the levels of AHLs in biofilms in drinking water distribution systems (DWDSs) and their impact on biofilm formation remain poorly understood. Herein, we simulated DWDSs via biofilm reactors to explore the presence and influence of AHLs during the initial stages of biofilm formation on pipe walls. Glass, polypropylene random copolymer (PP-R) and stainless steel (SS) were used as the coupon materials and the three parallel experimental groups were set up and named accordingly. The glass material is considered to form biofilms only minimally and is therefore used as a negative control. By day 30, the concentration of AHLs in biofilm phase in both PP-R group and SS group reached 1200-1800 ng/L. The predominant AHLs were C6-HSL, C8-HSL, and C10-HSL, with a significant positive correlation between AHLs and biofilm biomass. Metagenomic analysis revealed that microbes exhibiting significant differences among the three groups all demonstrated notable correlations with AHLs. Subsequent analysis of QS genes revealed that the genes associated with AHLs biosynthesis and QS receptors were more abundant in the PP-R and SS groups with biofilm formation. Additionally, we analyzed the abundance of genes related to cell motility, transmembrane transport, tricarboxylic acid cycle, and genetic information synthesis. The co-occurrence network indicates that these processes exhibit a strong correlation with QS genes. This study demonstrates the pivotal role of AHLs in microbial communication during the initial stages of biofilm formation in DWDSs and indicates that the regulatory pathways and mechanisms of AHLs may vary under different environmental conditions.},
}
@article {pmid39647535,
year = {2024},
author = {Casañas-Martínez, M and Barbero-Herranz, R and Alegre-González, D and Mosquera-Lozano, JD and Campo, RD and , },
title = {Fecal Microbiota Transplantation in a Long-Standing Auto-Brewery Syndrome with Complex Symptomatology.},
journal = {Journal of hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhep.2024.12.005},
pmid = {39647535},
issn = {1600-0641},
}
@article {pmid39647426,
year = {2024},
author = {Ge, H and Li, C and Huang, C and Zhao, L and Cong, B and Liu, S},
title = {Bacterial community composition and metabolic characteristics of three representative marine areas in northern China.},
journal = {Marine environmental research},
volume = {204},
number = {},
pages = {106892},
doi = {10.1016/j.marenvres.2024.106892},
pmid = {39647426},
issn = {1879-0291},
abstract = {Bacteria are essential components of ecosystems, participating in nutrient cycling and biogeochemical processes, and playing a crucial role in maintaining the stability of marine ecosystems. However, the biogeographic distribution patterns of bacterial diversity and metabolic functions in the estuarine and coastal areas of northern China remain unclear. Here, we used metagenomic sequencing to investigate the bacterial community composition and metabolic functions in sediments from the adjacent waters of the Yellow River Estuary, the Yellow Sea Cold Water Mass, and the adjacent waters of the Yangtze River Estuary. Among the 9164 species that were found, the most dominant microbial communities are Pseudomonadota, Actinomycetota, Bacteroidota, and Bacillota, but there are significant differences in the species composition in these three typical habitats. Amino acid metabolism and carbohydrate metabolic pathways were highly enriched. Glycoside hydrolases (GHs) predominate in carbon metabolism across all samples. In nitrogen metabolic pathway, genes related to organic degradation and synthesis are more abundant in the Yellow River Estuary than the other two habitats. In sulfur metabolic pathway, genes involved in assimilatory sulfate reduction are significantly enriched. Assimilatory sulfate reduction might be crucial for sulfur metabolism in coastal regions, with a full assimilatory nitrate reduction pathway found in Desulfobacterota. This research offers insights into the compositional diversity, metabolic functions, and biogeographic distribution patterns of bacterial communities in sediments from typical marine areas of northern China.},
}
@article {pmid39647412,
year = {2024},
author = {He, T and Xie, J and Jin, L and Zhao, J and Zhang, X and Liu, H and Li, XD},
title = {Seasonal dynamics of the phage-bacterium linkage and associated antibiotic resistome in airborne PM2.5 of urban areas.},
journal = {Environment international},
volume = {194},
number = {},
pages = {109155},
doi = {10.1016/j.envint.2024.109155},
pmid = {39647412},
issn = {1873-6750},
abstract = {Inhalable microorganisms in airborne fine particulate matter (PM2.5), including bacteria and phages, are major carriers of antibiotic resistance genes (ARGs) with strong ecological linkages and potential health implications for urban populations. A full-spectrum study on ARG carriers and phage-bacterium linkages will shed light on the environmental processes of antibiotic resistance from airborne dissemination to the human lung microbiome. Our metagenomic study reveals the seasonal dynamics of phage communities in PM2.5, their impacts on clinically important ARGs, and potential implications for the human respiratory microbiome in selected cities of China. Gene-sharing network comparisons show that air harbours a distinct phage community connected to human- and water-associated viromes, with 57 % of the predicted hosts being potential bacterial pathogens. The ARGs of common antibiotics, e.g., peptide and tetracycline, dominate both the antibiotic resistome associated with bacteria and phages in PM2.5. Over 60 % of the predicted hosts of vARG-carrying phages are potential bacterial pathogens, and about 67 % of these hosts have not been discovered as direct carriers of the same ARGs. The profiles of ARG-carrying phages are distinct among urban sites, but show a significant enrichment in abundance, diversity, temperate lifestyle, and matches of CRISPR (short for 'clustered regularly interspaced short palindromic repeats') to identified bacterial genomes in winter and spring. Moreover, phages putatively carry 52 % of the total mobile genetic element (MGE)-ARG pairs with a unique 'flu season' pattern in urban areas. This study highlights the role that phages play in the airborne dissemination of ARGs and their delivery of ARGs to specific opportunistic pathogens in human lungs, independent of other pathways of horizontal gene transfer. Natural and anthropogenic stressors, particularly wind speed, UV index, and level of ozone, potentially explained over 80 % of the seasonal dynamics of phage-bacterial pathogen linkages on antibiotic resistance. Therefore, understanding the phage-host linkages in airborne PM2.5, the full-spectrum of antibiotic resistomes, and the potential human pathogens involved, will be of benefit to protect human health in urban areas.},
}
@article {pmid39647330,
year = {2024},
author = {Xu, H and Zhu, D and Zhong, M and Li, C and Wen, C and Zhu, S and Li, Q and Luo, X},
title = {Source-oriented risks of heavy metals and their effects on resistance genes in natural biofilms.},
journal = {Journal of hazardous materials},
volume = {484},
number = {},
pages = {136735},
doi = {10.1016/j.jhazmat.2024.136735},
pmid = {39647330},
issn = {1873-3336},
abstract = {Heavy metal (HM) introduction from various land-use patterns can be a major source of metal resistance genes (MRGs) entering river environments. This influx can trigger the occurrence of other resistomes, such as antibiotic resistance genes (ARGs), by improving co-resistant conjugative transfer. Biofilms, which form at water-solid interfaces, could serve as potential hotspots for HMs and resistance genes. However, the enrichment of HMs from various sources within biofilms and their effect on resistomes remain undocumented. This study aims to investigate the physicochemical properties of biofilm samples collected from the Heihui River, a tributary of the Lancang River, and to analyze the concentrations of nine HMs (As, Cd, Co, Cr, Cu, Ni, Pb, V, and Zn) within these biofilms. The 16S rRNA gene and metagenomic high-throughput sequencing techniques were integrated to uncover the association between HM accumulation levels in biofilms and ecological and health risks, considering the presence of two resistance genes. Natural sources (Co, Cr), industrial (As, Cu, V), agricultural (Cd, Ni), and transportation activities (Pb, Zn) markedly contributed to HM presence within biofilms, with industrial activities posing higher noncarcinogenic and carcinogenic risks than other sources. The network-correlation analyses revealed higher levels of ARG-MRG coexistence in biofilms, with the ecological and health risk index of HMs in biofilms closely associated with the abundance of both resistance genes. Furthermore, the biofilm As concentration markedly affected the abundance and expression of ARGs and MRGs, with elevated As levels within biofilms significantly and positively influencing all four functional categories of MRGs. Water pH also indirectly impacted these functional types by modulating the ionic form of HMs within the biofilm matrix. Our findings underscore the significance of integrating biofilms into environmental management practices and standards for assessing environmental quality.},
}
@article {pmid39647263,
year = {2024},
author = {Fu, Y and Gou, W and Zhong, H and Tian, Y and Zhao, H and Liang, X and Shuai, M and Zhuo, LB and Jiang, Z and Tang, J and Ordovas, JM and Chen, YM and Zheng, JS},
title = {Diet-gut microbiome interaction and its impact on host blood glucose homeostasis: a series of nutritional n-of-1 trials.},
journal = {EBioMedicine},
volume = {111},
number = {},
pages = {105483},
doi = {10.1016/j.ebiom.2024.105483},
pmid = {39647263},
issn = {2352-3964},
abstract = {BACKGROUND: The interplay between diet and gut microbiome substantially influences host metabolism, but uncertainties remain regarding their relationships tailored for each subject given the huge inter-individual variability. Here we aim to investigate diet-gut microbiome interaction at single-subject resolution and explore its effects on blood glucose homeostasis.<br><br>METHODS: We conducted a series of nutritional n-of-1 trials (NCT04125602), in which 30 participants were assigned high-carbohydrate (HC) and low-carbohydrate (LC) diets in a randomized sequence across 3 pair of cross-over periods lasting 72 days. We used shotgun metagenomic sequencing and continuous glucose monitoring systems to profile the gut microbiome and blood glucose, respectively. An independent cohort of 1219 participants with available metagenomics data are included as a validation cohort.<br><br>FINDINGS: We demonstrated that the gut microbiome exhibited both intra-individually dynamic and inter-individually personalized signatures during the interventions. At the single-subject resolution, we observed person-specific response patterns of gut microbiota to interventional diets. Furthermore, we discovered a personal gut microbial signature represented by a carb-sensitivity score, which was closely correlated with glycemic phenotypes during the HC intervention, but not LC intervention. We validate the role of this score in the validation cohort and find that it reflects host glycemic sensitivity to the personal gut microbiota profile when sensing the dietary carbohydrate inputs.<br><br>INTERPRETATION: Our finding suggests that the HC diet modulates gut microbiota in a person-specific manner and facilitates the connection between gut microbiota and glycemic sensitivity. This study represents a new paradigm for investigating the diet-microbiome interaction in the context of precision nutrition.<br><br>FUNDING: This work was supported by the National Key R&amp;D Program of China, National Natural Science Foundation of China and Zhejiang Provincial Natural Science Foundation of China.},
}
@article {pmid39644935,
year = {2024},
author = {Chu, Z and Tang, X and Li, Y and Li, J and Xiong, W and Yin, Y and Pan, X},
title = {Simultaneous removal of organic matter and inorganic nitrogen in Baijiu wastewater by methanotrophic denitrification.},
journal = {Bioresource technology},
volume = {418},
number = {},
pages = {131956},
doi = {10.1016/j.biortech.2024.131956},
pmid = {39644935},
issn = {1873-2976},
abstract = {Methanotroph could facilitate nitrogen removal during methane oxidation, and promote conversion of organic compounds by producing methane monooxygenase. Co-metabolic effect and mechanism of aerobic methane oxidation on the removal of nitrogen and organic matter from Baijiu wastewater were investigated using an improved denitrifying biological filter. It was found that the average removal efficiency of chemical oxygen demand (COD), total nitrogen (TN) and chroma increased by 17 %, 22 % and 10 % in reactor B with methane compared to reactor A with air only. Three-dimensional fluorescence spectroscopy and Fourier transform infrared spectroscopy analysis revealed that methanotroph co-metabolism was accompanied by eliminating nitrogen and organic matter as well as forming alcohol compounds. Metagenomic analyses revealed that Methylocaldum, the dominant genera in Reactor B, exerted a pivotal role in removing nitrogen and organic matter removal by supplying energy and catalysis. Functional genes pmoABC-amoABC could facilitate nitrogen and organic matter removal.},
}
@article {pmid39644909,
year = {2024},
author = {Mäklin, T and Taira, A and Arredondo-Alonso, S and Shao, Y and Stratton, MR and Lawley, TD and Aaltonen, LA and Corander, J},
title = {Geographical variation in the incidence of colorectal cancer and urinary tract cancer is associated with population exposure to colibactin-producing Escherichia coli.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101015},
doi = {10.1016/j.lanmic.2024.101015},
pmid = {39644909},
issn = {2666-5247},
abstract = {Biomedical research has implicated the bacterial metabolite colibactin as a causal risk factor for several cancer types, in particular, colorectal cancer. Colibactin has been known to drive tumorigenesis by inducing double-strand breaks in the DNA of epithelial cells exposed to colibactin-producing bacteria. Some phylogroup B2 Escherichia coli secrete colibactin during interbacterial warfare, concomitantly exposing the host to an increasing risk of DNA damage. This Personal View reviews the current knowledge about the cancer-colibactin interface and summarises metagenomics-based and population-genomics-based surveys to show that the prevalence of dominant colibactin-producing lineages of E coli varies considerably across geographical regions. The prevalence is further strongly associated with the age-standardised incidences of colorectal cancer, bladder cancer, and prostate cancer, suggesting that the degree of colibactin exposure in a population might contribute to the geographical variation of these cancers. Our observations provide a strong impetus for further research and the development of novel interventions to reduce the risks for colibactin-related cancers.},
}
@article {pmid39644836,
year = {2024},
author = {Wang, L and Wang, X and Wu, H and Fan, S and Lu, Z},
title = {Integration of metagenomic analysis and metabolic modeling reveals microbial interactions in activated sludge systems in response to nanoplastics and plasticizers.},
journal = {Water research},
volume = {271},
number = {},
pages = {122863},
doi = {10.1016/j.watres.2024.122863},
pmid = {39644836},
issn = {1879-2448},
abstract = {Nanoplastics and plasticizers are prevalent in activated sludge and pose a potential threat to microbial communities in wastewater treatment systems. However, studies on the effects of nanoplastics and plasticizers on the interaction mechanisms and metabolic functions of microbial communities in activated sludge systems are still scarce. In this study, the responses of microbial interactions and metabolic functions to PVC nanoplastics (PVCNPs) and bis(2-ethylhexyl) phthalate (DEHP) in activated sludge were investigated via a combination of amplicon sequencing, metagenome sequencing, and metabolic modeling. The results revealed that DEHP had a significant effect on the microbial community under short-term exposure. DEHP contamination may increase vitamin B12 producers to enhance species collaboration in communities. Furthermore, community metabolic modeling revealed that DEHP-degrading bacteria could promote positive interactions among community members. The increased metabolic exchange flux of siderophores and glutathione in microbial communities under PVCNPs and DEHP contamination implied that microbial communities may maintain iron homeostasis in response to PVCNPs and DEHP contamination through interspecies collaboration. However, more data are needed to further validate these results. This study provides vital insights into the response mechanisms of microbial interactions to nanoplastic and plasticizer contamination in activated sludge systems.},
}
@article {pmid39644773,
year = {2024},
author = {Hu, Y and Hu, X and Jiang, L and Luo, J and Huang, J and Sun, Y and Qiao, Y and Wu, H and Zhou, S and Li, H and Li, J and Zhou, L and Zheng, S},
title = {Microbiome and metabolomics reveal the effect of gut microbiota on liver regeneration of fatty liver disease.},
journal = {EBioMedicine},
volume = {111},
number = {},
pages = {105482},
doi = {10.1016/j.ebiom.2024.105482},
pmid = {39644773},
issn = {2352-3964},
abstract = {BACKGROUND: Metabolic dysfunction-associated fatty liver disease (MAFLD) is associated with impaired regenerative capacity and poor postoperative prognosis following hepatectomy. Previous research has highlighted the importance of the gut-liver axis in the physiological and pathological processes of the liver. However, the contribution of gut bacteria to the regeneration of livers with MAFLD and its metabolic regulatory mechanisms remain elusive.<br><br>METHODS: Partial hepatectomy (PHx) was performed on C57Bl/6J mice fed with high-fat diet (HFD) for 12 weeks. Pathological examination, immunohistochemistry, and qRT-PCR analysis were performed to assess the severity of steatosis and proliferative potential. The gut microbiome was examined by 16S rRNA gene sequencing and shotgun metagenomics, whereas liver metabolomics was analysed via untargeted and targeted metabolomics using liquid chromatography-tandem mass spectrometry (LC-MS).<br><br>FINDINGS: HFD-induced hepatic steatosis in mice led to impaired liver regeneration following PHx. The gut microbiota and liver metabolites were altered along with the liver regeneration process. Longitudinal time-series analysis revealed dynamic alterations in these data, whereas correlation analysis screened out bacterial candidates that potentially influence liver regeneration in MAFLD by modulating metabolic pathways. Among these bacteria, the dominant bacterium Akkermansia was selected for subsequent investigation. MAFLD mice gavaged with Akkermansia muciniphila (A.&#xa0;muciniphila) exhibited reduced liver lipid accumulation and accelerated liver regeneration, possibly through the regulation of the tricarboxylic acid (TCA) cycle.<br><br>INTERPRETATION: These data demonstrated the interplay between the gut microbiome, liver metabolomics, and liver regeneration in mice with MAFLD. A.&#xa0;muciniphila has the potential to serve as a clinical intervention agent to accelerate postoperative recovery in MAFLD.<br><br>FUNDING: This work was supported by the Research Project of Jinan Microecological Biomedicine Shandong Laboratory [JNL-2022008B]; the Zhejiang Provincial Natural Science Foundation of China [LZ21H180001]; the Fundamental Research Funds for the Central Universities [No. 2022ZFJH003].},
}
@article {pmid39644571,
year = {2024},
author = {Zhou, X and Li, Q and Shi, Z and Lu, W and Shu, C and Zhu, J and Wu, Y},
title = {Assessing the prevalence of human enteric viruses in hospital wastewater to evaluate the effectiveness of wastewater treatment systems.},
journal = {Ecotoxicology and environmental safety},
volume = {289},
number = {},
pages = {117488},
doi = {10.1016/j.ecoenv.2024.117488},
pmid = {39644571},
issn = {1090-2414},
abstract = {In this experiment, we employed Real-time PCR(RT-PCR) and metagenomic Next-Generation Sequencing (mNGS) techniques to detect the presence of Norovirus, Rotavirus Group A, Adenovirus Group F, and Astrovirus in untreated sewage from three major hospitals. A comparison with clinical lab test outcomes revealed Norovirus as having the highest infection rate, followed by Adenovirus Group F and Rotavirus Group A. Despite not testing for Astrovirus in clinical labs, its sewage detection rate was surpassed only by Norovirus, suggesting a potentially high clinical infection rate. Further analysis of these viruses in treated sewage revealed that chlorination failed to eliminate the virus, maintaining viral concentrations in the treated sewage between 10^2 and 10^3 copies/ml. Even though nucleic acid testing methods fail to detect viral actions, the possible danger they present to public safety should not be ignored. During this experiment, viral nucleic acid was extracted directly from the samples without prior concentration. This method, unlike conventional virus detection post-concentration, bypasses concerns such as recovery efficiency, offering a clearer representation of virus concentrations in water samples and facilitating easier operation.},
}
@article {pmid39644540,
year = {2024},
author = {Xiong, W and Dong, L and Zhu, N and Zhou, D and Li, S and Lv, J and Xu, M and Zhang, Y and Li, S},
title = {The diagnostic value of metagenomic next-generation sequencing in suspected pulmonary tuberculosis patients with scarce sputum or negative sputum etiological test results.},
journal = {Diagnostic microbiology and infectious disease},
volume = {111},
number = {3},
pages = {116633},
doi = {10.1016/j.diagmicrobio.2024.116633},
pmid = {39644540},
issn = {1879-0070},
abstract = {OBJECTIVE: To compare the diagnostic value between mNGS and conventional tests in suspected pulmonary tuberculosis (PTB) patients with scarce sputum or with negative sputum etiological test results.<br><br>METHODS: We enrolled eligible patients admitted to our department from 2018 to 2021. Their bronchoalveolar lavage fluid (BALF) and lung biopsy tissue samples were sent for mNGS and conventional tests. The diagnostic value of mNGS was compared respectively with that of conventional tests.<br><br>RESULTS: 94 of 226 enrolled patients were diagnosed PTB. The diagnostic concordance rate of mNGS was significantly higher than that of acid-fast staining in all samples (p < 0.001), as well as that of culture in BALF samples (p = 0.011). mNGS in parallel with conventional tests had significantly higher AUC than mNGS alone (p = 0.013).<br><br>CONCLUSIONS: mNGS has higher diagnostic value than some conventional tests. mNGS in parallel with conventional tests is more reliable to accurately diagnose these suspected PTB patients.},
}
@article {pmid39644431,
year = {2024},
author = {Kara, K and Pi Rci, G and Yılmaz Öztaş, S and Demi R, S and Yılmaz, K},
title = {Effect of milk thistle (Silybum marianum L.) oil on pro-inflammatory cytokines, acute phase proteins, rumen metagenomic profile, rumen fluid variables and performance in calves.},
journal = {Veterinary research communications},
volume = {49},
number = {1},
pages = {48},
pmid = {39644431},
issn = {1573-7446},
support = {TSA-2023-12255//Bilimsel Ara&#x15f;t&#x131;rma Projeleri, Erciyes &#xdc;niversitesi/ ; },
mesh = {Animals ; Cattle ; *Rumen/microbiology ; Female ; Male ; *Cytokines/metabolism/genetics ; *Plant Oils/pharmacology/administration &amp; dosage ; *Acute-Phase Proteins/metabolism ; *Silybum marianum/chemistry ; *Diet/veterinary ; Dietary Supplements/analysis ; Animal Feed/analysis ; },
abstract = {The aim of this study was to determine the effect of milk thistle (Silybum marianum L., SM) oil supplementation on proinflammatory cytokines, acute phase proteins, rumen metagenomic profile, rumen fluid variables and performance during the milk feeding period of Holstein calves. In the present study, 24 calves that consumed quality and sufficient amount of colostrum (≥50 mg/ml IgG) after birth were divided into three groups, with 8 animals in each group (4 males + 4 females). Individually fed calves were given added SM oil as 0 µL/day/calf (Control group, SM0), 100 µL/day/calf (SM100) and 200 µL/day/calf (SM200). The ration containing concentrated feed mix (90%) + wheat straw (10%) was offered to the calves. SM oil did not change the ammonia nitrogen and pH values of the rumen fluid of calf (P>0.05). The molarities of PA, IBA, IVA and BSCFA in the rumen fluid increased linearly with SM oil dose (P<0.05). The relative abundance of Firmicutes linearly increased and the relative abundance of Actinobacteriota decreased with the addition of SM oil (P<0.05). Relative abundances of Erysipelotrichaceae_UCG_002, Eubacterium_coprostanoligenes_group, Clostridia_UCG_014, Lachnospiraceae_Unknown_1, Lachnospiraceae_NK3A20_group, Shuttleworthia, Selenomonadaceae_Uncultured_1, Rikenellaceae_RC9_gut_group and Succinivibrionaceae_UCG_001 linearly increased with SM oil (P<0.05). Relative abundances of Methanobrevibacter, Acetitomaculum, Olsenella and Megasphaera in calf rumen fluid linearly decreased with SM oil (P<0.05). Concentrations of TNF-α, IFN-ɣ, and SAA of calf' serum at weaning stage linearly decreased with SM oil doses (P<0.05). Serum IgA concentration increased with 100 µL SM oil /day (P<0.05). As a result, the addition of SM oil to calves has the potential to reduce the immune suppression of calves during the milk feeding period and at weaning time, has a positive effect on the microbiome involved in starch and protein catabolism in the rumen fluid, and increases the fermentation end products (PA, IVA and BA). Milk thistle oil has an inhibitory effect on methanogenic archaea and can be used as an anti-methanogenic feed additive and will contribute to the effective use of feed energy.},
}
@article {pmid39643877,
year = {2024},
author = {Cui, Z and Wang, S and Niu, J and Ma, J and Yang, H},
title = {Bifidobacterium species serve as key gut microbiome regulators after intervention in gestational diabetes mellitus.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {520},
pmid = {39643877},
issn = {1471-2180},
support = {22cz020401-4811009//National High Level Hospital Clinical Research/ ; 81830044//National Natural Science Foundation of China/ ; 2021YFC2700700//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Diabetes, Gestational/microbiology/metabolism/blood ; Pregnancy ; *Gastrointestinal Microbiome/genetics ; Female ; *Bifidobacterium/genetics ; Adult ; *Feces/microbiology ; Fatty Acids, Volatile/metabolism ; Dysbiosis/microbiology ; Genome-Wide Association Study ; Metagenome ; },
abstract = {Gut microbiome dysbiosis is associated with gestational diabetes mellitus (GDM), and its modulation represents a promising approach for enhancing glycemic control. In this study, we aimed to discover specific alterations in the gut microbiome through lifestyle management. We performed metagenome sequencing on fecal samples and measured short-chain fatty acid (SCFA) in plasma samples from 27 well-controlled GDM pregnancies before and after glycemic control. At the same time, 38 normal glucose tolerance (NGT) samples served as controls. Additionally, we employed two-sample Mendelian Randomization (MR) to validate our findings against Genome-Wide Association Study (GWAS) database. Our dynamic analysis revealed Bifidobacterium genus increased in GDM patients after intervention. The MR analysis confirmed that the family of Bifidobacteriaceae (OR 0.929, 95% CI, 0.886-0.975; P = 0.003) was the only negatively associated family with GDM. Further analysis indicated the increased abundance of Bifidobacterium species were negatively correlated with glycemic traits (Spearman rho mean - 0.32 ± 0.34) but positively correlated with plasma SCFA levels (Spearman rho mean 0.24 ± 0.19). Functional analysis revealed that the quorum-sensing pathway had the strongest effect on the ability of Bifidobacterium to promote glucose homeostasis (Spearman rho = -0.34), suggesting its role in regulating intestinal microbiota. Finally, the multivariable MR analysis demonstrated that two pathways, COLANSYN PWY and PWY 7323, responsible for cell surface compound synthesis in gram-negative bacteria, mediated 14.83% (P = 0.017) and 16.64% (P = 0.049) of the protective effects of Bifidobacteriaceae against GDM, respectively. In summary, Bifidobacterium is an effective gut microbiota regulator for GDM-related glucose homeostasis.},
}
@article {pmid39643526,
year = {2024},
author = {Yen, TY and Hsu, C and Lee, NC and Wu, CS and Wang, H and Lee, KY and Lin, CR and Lu, CY and Tsai, ML and Liu, TY and Lin, C and Chen, CY and Chang, LY and Lai, F and Huang, LM},
title = {Signatures of lower respiratory tract microbiome in children with severe community-acquired pneumonia using shotgun metagenomic sequencing.},
journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jmii.2024.11.011},
pmid = {39643526},
issn = {1995-9133},
abstract = {BACKGROUND: Severe community-acquired pneumonia was associated with high morbidity and mortality in children. However, species-level microbiome of lower airway was sparse, and we used shotgun metagenomic next-generation sequencing to explore microbial signatures.<br><br>METHODS: We conducted a prospective cohort study to recruit children under 18 who required admission to an intensive care unit for community-acquired pneumonia between December 2019 and February 2022. Lower respiratory specimens were collected on admission for shotgun metagenomic sequencing. The children were divided into two groups. Critical cases were patients with respiratory failure requiring endotracheal ventilator support, and severe cases did not require intubation. Signatures of lower respiratory tract microbiome were compared between groups using an exact k-mer matching metagenomic analysis pipeline (Kraken 2) and a metagenome-assembled genomes pipeline (MetaWRAP).<br><br>RESULTS: Totally 66 children were enrolled, and 27 children were critical cases, and the rest were severe cases. There were significant differences in microbial community structure between different severity groups, and microbial abundance was negatively correlated with disease severity. The results showed that Haemophilus influenzae was more prominent in children who were critical, accompanied with increased expression of intracellular transport, secretion, and vesicle transport genes. Rothia mucilaginosa, Dolosigranulum pigrum, and Prevotella melaninogenica tended to be present in less severe community-acquired pneumonia group.<br><br>CONCLUSION: This study demonstrated that significantly different microbial community was associated with severity of community-acquired pneumonia requiring intensive care admission. Species-level shotgun metagenomic sequencing facilitates the exploration of potentially pathogenic or protective microbes and shed the light of probiotic development in lower respiratory tract.},
}
@article {pmid39643486,
year = {2024},
author = {Reyes-Sosa, MB and Valle-Gough, R and Ponce-Caballero, MDC and Arena-Ortiz, ML},
title = {Bacterial richness assessment in water and sediments in the northern coast of the Yucatan Peninsula.},
journal = {Revista Argentina de microbiologia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ram.2024.10.009},
pmid = {39643486},
issn = {0325-7541},
abstract = {Given the importance of the coastal environments and the multiple ecological services that they provide, it is important to explore and understand the interactions that occur within them. The microbiome is a key factor for the understanding of the dynamics of these fragile sites. A metagenomic study based on the profiling of the 16S ribosomal gene was carried out in order to assess the bacterial diversity present in the northern coastal zone of the Yucatan Peninsula. The results showed that water and sediment samples share some similarities regarding the bacterial genera found, only differing in the quantitative part. Through a PCO (principal coordinates) analysis clear differences between sediment and water samples could be observed. The highest relative diversity was found in wetland and lagoon sediment samples, respectively. It was observed that 3-8% of the total sequence reads belonged to opportunistic genera such as: Vibrio in the sea samples and Capnocytophaga in the other environments. Salinity and pH were the factors which contributed the most to the differences among the communities in the various environments in the coastal zone. There is an important similarity in the sediments across the different environments within the studied coastal zone. The data presented herein contribute to setting a baseline for research in the coastal region of the Yucatan Peninsula.},
}
@article {pmid39643362,
year = {2024},
author = {Shen, C and Yu, Y and Zhang, X and Zhang, H and Chu, M and Yuan, B and Guo, Y and Li, Y and Zhou, J and Mao, J and Xu, X},
title = {The dynamic of physicochemical properties, volatile compounds and microbial community during the fermentation of Chinese rice wine with diverse cereals.},
journal = {Food research international (Ottawa, Ont.)},
volume = {198},
number = {},
pages = {115319},
doi = {10.1016/j.foodres.2024.115319},
pmid = {39643362},
issn = {1873-7145},
mesh = {*Wine/analysis/microbiology ; *Fermentation ; *Volatile Organic Compounds/analysis ; *Oryza/chemistry ; *Odorants/analysis ; Microbiota ; Edible Grain/chemistry/microbiology ; Gas Chromatography-Mass Spectrometry ; Taste ; Amino Acids/analysis/metabolism ; Esters/analysis/metabolism ; Bacteria/classification/metabolism ; East Asian People ; },
abstract = {This study investigates the impact of liquid state fermentation on the key flavor compounds and microbial community structure in Chinese rice wine brewed from five different raw materials: buckwheat, sorghum, japonica rice, glutinous rice, and black rice. Using HS-SPME-GC-MS and HPLC, the volatile compounds were analyzed across various grain liquefaction methods, detecting 82 volatiles, including esters, alcohols, aldehydes, and acids. The concentration of flavor compounds such as esters, amino acids, phenolic acids, and organic acids varied significantly depending on the raw material used. Based on odor activity values, 31 key compounds were identified, including 15 ethyl esters, like ethyl laurate, responsible for the unique and complex aroma of the rice wines. Bitter amino acids, making up over 50 % of the total amino acids, were predominant. Among the varieties, the buckwheat-fermented wine exhibited the highest ester content (27.39 mg/L), nearly double that of other samples, along with elevated amino acids (1.47 mg/mL) and phenolic acids (904.29 mg/L). Black rice ranked second in amino acid content (0.93 mg/mL), while glutinous rice had the highest organic acid content (239.76 mg/mL). Metagenomic sequencing on the fifth day of fermentation revealed significant differences in microbial community structure among the raw materials. Saccharomyces, Aspergillus, Thermomyces, Epicoccus, and Albertella were dominant fungi, while Weissella, Thermoactinomyces, Bacillus, and Saccharopolyspora were dominant bacteria. Sensory analysis showed that buckwheat-fermented rice wine was distinguished by its honey, floral, creamy, and umami attributes, while balancing alcohol, acidity, bitterness, and Qu aroma. The results demonstrate the significant influence of raw material selection and liquefaction method on both flavor profile and microbial diversity in Chinese rice wine.},
}
@article {pmid39643360,
year = {2024},
author = {Li, N and Xu, W and Meng, L and Zhao, Y and Zhao, X and Zheng, N and Zhang, Y and Wang, J},
title = {Metagenomics reveals differences in spore-forming bacterial diversity in raw milk in different regions and seasons in China.},
journal = {Food research international (Ottawa, Ont.)},
volume = {198},
number = {},
pages = {115317},
doi = {10.1016/j.foodres.2024.115317},
pmid = {39643360},
issn = {1873-7145},
mesh = {*Seasons ; Animals ; *Milk/microbiology ; China ; *Spores, Bacterial/genetics ; *Metagenomics ; Food Microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; Biodiversity ; },
abstract = {The spore-forming bacteria in the dairy industry are notable for their spores resilience and capacity to survive heating processes, allowing them to germinate and enter the vegetative stage, potentially leading to spoilage of the milk. Additionally, these spores can form biofilms, becoming a persistent source of contamination in processing environments. In this study, we collected a total of 165 raw milk from six different parts in China in spring, summer, autumn, and winter, respectively. Metagenomics sequencing method was used to explore and compare the differences in spore-forming bacterial composition and diversity in raw milk samples. Among these samples, four genera and 207 species of spore-forming bacteria were identified, with the genus Bacillus and the species Paenibacillus darwinianus dominant. Seasonal variations had a greater impact on the composition and abundance of spore-forming bacteria in raw milk than regional differences. Notable, raw milk samples collected during the spring and summer exhibited a higher number of unique spore-forming bacterial species compared to those collected in other seasons. Moreover, different regions and seasons have their own dominant bacteria. Metabolism of cofactors and vitamins, energy metabolism, carbohydrate metabolism, and amino acid metabolism were the main metabolic pathways. Hence, specific strategies need to be adopted to prevent and control spore-forming bacteria in raw milk in different regions and seasons.},
}
@article {pmid39643345,
year = {2024},
author = {Jian, C and Sun, M and Ma, T and Wang, W and Lv, B and Wang, J and Su, X and Li, S and Guo, Y},
title = {Revealing the formation mechanisms of key flavor components during the fermentation of bamboo shoots by combining flavoromics and metagenomics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {198},
number = {},
pages = {115361},
doi = {10.1016/j.foodres.2024.115361},
pmid = {39643345},
issn = {1873-7145},
mesh = {*Fermentation ; *Metagenomics ; *Taste ; *Volatile Organic Compounds/analysis/metabolism ; *Odorants/analysis ; *Metabolomics ; Flavoring Agents/metabolism ; Plant Shoots ; Fermented Foods/microbiology ; Bacteria/genetics/classification/metabolism ; Food Microbiology ; Amino Acids/analysis/metabolism ; Microbiota ; },
abstract = {Microbial metabolism plays a critical role in the flavor development of Guangxi fermented bamboo shoots (GFBS). To clarify the role of microorganisms in flavor formation and predict the metabolic pathways of key characteristic flavor compounds, this study employed metabolomics, Odor Activity Value (OAV), and Taste Activity Value (TAV) calculations, integrated with Partial Least Squares Discriminant Analysis (PLS-DA), to investigate changes in GFBS flavors-represented by volatile flavor compounds, organic acids, and free amino acids-across a 30-day fermentation period. Metagenomic datasets were used to identify taxonomic and functional changes in the microbial community. As a result, 26 characteristic flavor compounds (OAV or TAV > 1) were identified in mature GFBS, and 23 differential flavor compounds were identified at different fermentation stages using PLS-DA (VIP > 1.2). The top 10 microbial genera associated with these characteristic flavor compounds were identified, including Acinetobacter, Enterobacter, Raoultella, Enterococcus, Klebsiella, Lactococcus, Leuconostoc, Weissella, Lactiplantibacillus and Limosilactobacillus. Based on these findings, a predictive metabolic network of key flavor compounds in GFBS was constructed, providing a comprehensive understanding of the diverse metabolic roles of microorganisms during fermentation. This work lays a theoretical foundation for the standardized production and quality control of GFBS flavor.},
}
@article {pmid39643336,
year = {2024},
author = {Li, T and Cao, W and Li, D and Wei, C and Yan, Y and Zeng, X},
title = {Metagenomic insights into quorum sensing-associated microbial profiling and its correlations with flavor compounds of Maotai-flavor liquor: A case study of stacking fermented grains.},
journal = {Food research international (Ottawa, Ont.)},
volume = {198},
number = {},
pages = {115324},
doi = {10.1016/j.foodres.2024.115324},
pmid = {39643336},
issn = {1873-7145},
mesh = {*Quorum Sensing ; *Fermentation ; *Flavoring Agents/metabolism ; *Metagenomics/methods ; Taste ; Food Microbiology ; Bacteria/genetics/metabolism/classification ; Fungi/genetics/metabolism ; Edible Grain/microbiology ; Alcoholic Beverages/microbiology ; Microbiota ; },
abstract = {Stacking fermentation is typical process of Maotai-flavor Baijiu and microbial composition determine content of flavors. To date, the knowledge on the driving force of microbial composition was as yet unknown. Since quorum sensing molecule (QSM) plays an important role in modifying microbial interactions. Therefore, the objectives of the present study were: (1) to describe the microbial profile associated with QSM in stacking grains using metagenomics; (2) to elucidate how QSM shapes microbial interactions and accordingly regulates flavor synthesis. Results indicated that bacterial QSM including AI-2, DSF, and AHL as well as fungal QSM aromatic alcohols and farnesol were prevalent in the stacking fermented grains. Thereinto, AI-2 might be an important driving force of microbial composition due to its highest abundance. AI-2 in Limosilactobacillus fermentum, Pediococcus pentosaceus, and Weissella cibaria perhaps modified microbial interactions together with fungal QSM in Schizosaccharomyces pombe and Pichia membranifaciens. The role of AI-2 was much higher than that of fungal QSM. Furthermore, QSM indirectly influenced the synthesis of important flavors such as ethyl lactate, phenylethanol, and ethyl phenylacetate through the dynamic of microbial composition. Together, this current study for the first time explored the effects of QSM on microbial composition and flavor synthesis in the Baijiu field.},
}
@article {pmid39643156,
year = {2024},
author = {Wang, Y and Zeng, T and Tang, D and Cui, H and Wan, Y and Tang, H},
title = {Integrated Multi-Omics Analyses Reveal Lipid Metabolic Signature in Osteoarthritis.},
journal = {Journal of molecular biology},
volume = {},
number = {},
pages = {168888},
doi = {10.1016/j.jmb.2024.168888},
pmid = {39643156},
issn = {1089-8638},
abstract = {Osteoarthritis (OA) is the most common degenerative joint disease and the second leading cause of disability worldwide. Single-omics analyses are far from elucidating the complex mechanisms of lipid metabolic dysfunction in OA. This study identified a shared lipid metabolic signature of OA by integrating metabolomics, single-cell and bulk RNA-seq, as well as metagenomics. Compared to the normal counterparts, cartilagesin OA patients exhibited significant depletion of homeostatic chondrocytes (HomCs) (P=0.03) and showed lipid metabolic disorders in linoleic acid metabolism and glycerophospholipid metabolism which was consistent with our findings obtained from plasma metabolomics. Through high-dimensional weighted gene co-expression network analysis (hdWGCNA), weidentified PLA2G2A as a hub gene associated with lipid metabolic disorders in HomCs. And an OA-associated subtype of HomCs, namely HomC1 (marked by PLA2G2A, MT-CO1, MT-CO2, and MT-CO3) was identified, which also exhibited abnormal activation of lipid metabolic pathways. This suggests the involvement of HomC1 in OA progression through the shared lipid metabolism aberrancies, which were further validated via bulk RNA-Seq analysis. Metagenomic profiling identified specific gut microbial species significantly associated with the key lipid metabolism disorders, including Bacteroides uniformis (P<0.001, R=-0.52), Klebsiella pneumonia (P=0.003, R=0.42), Intestinibacter_bartlettii (P=0.009, R=0.38), and Streptococcus anginosus (P=0.009, R=0.38). By integrating the multi-omics features, a random forest diagnostic model with outstanding performance was developed (AUC=0.97). In summary, this study deciphered the crucial role of a integrated lipid metabolic signature in OA pathogenesis, and established a regulatory axis of gut microbiota-metabolites-cell-gene, providing new insights into the gut-joint axis and precision therapy for OA.},
}
@article {pmid39643107,
year = {2024},
author = {Khedpande, N and Barve, K},
title = {Role of gut dysbiosis in drug-resistant epilepsy: Pathogenesis and available therapeutic strategies.},
journal = {Brain research},
volume = {},
number = {},
pages = {149385},
doi = {10.1016/j.brainres.2024.149385},
pmid = {39643107},
issn = {1872-6240},
abstract = {Over 70 million people worldwide suffer from epilepsy, a persistent brain disorder. Although there are more than 20 antiseizure drugs available for the symptomatic treatment of epilepsy, about one-third of patients with epilepsy experience seizures that show resistance to pharmacotherapy. Since patients with drug-resistant epilepsy are more prone to physical injuries, psychosocial dysfunction, early death, and deteriorated life quality, the development of safer and more effective treatments is a crucial clinical need. The gut-brain axis and microbiome research advances have provided new insights into the pathophysiology of epilepsy, the resistance to anti-seizure medicine, and potential treatment targets. Inflammation, disturbance of the blood-brain barrier, and altered neurotransmitters are key pathways linked to gut dysbiosis. The characterization of microbial species and functional pathways has advanced thanks to metagenomic sequencing and high-throughput analysis. In this review, we elaborate on the gut-mediated molecular pathways involved in drug-resistant epilepsy, the gut- modulatory therapeutic options, and their combination with antiseizure medications for drug-resistant epilepsy.},
}
@article {pmid39642837,
year = {2024},
author = {Li, Y and Liu, K and Qiu, H and Chen, F and Zhang, J and Zheng, Z},
title = {Dynamics of antibiotic resistance genes and bacterial community structure within substrate biofilms.},
journal = {Journal of environmental management},
volume = {373},
number = {},
pages = {123512},
doi = {10.1016/j.jenvman.2024.123512},
pmid = {39642837},
issn = {1095-8630},
abstract = {Biofilms that develop on the surface of substrates are critical for treating wastewater. The accumulation of antibiotic resistance genes (ARGs) within these biofilms is particularly noteworthy. Despite their importance, studies that focus on biofilms attached to substrate surfaces remain scarce. This investigation explored the prevalence and succession of ARGs and microbial dynamics in biofilms on different substrates (ceramic, biomass filter, and steel slag) versus water biofilms over a year. Results showed distinct differences in ARG profiles between water and substrate biofilms. Multidrug ARGs constituted 39.14-46.73% of all ARGs in the substrate biofilms, with macrolide ARGs making up 11.98-14.52%. Seasonal variations influenced the diversity of the ARGs, notably increasing during the spring. The neutral community model suggested that the ARG assembly was dominantly driven by stochastic process. Proteobacteria, Actinobacteria and Campylobacter emerged as the predominant phyla within these biofilms. The microbial community distribution was predominantly influenced by ammonium nitrogen (NH4[+]-N) (R[2] = 0.4113), temperature and total nitrogen (TN). Notably, temperature exerted a critical impact on the microbial community distribution (P = 0.001), identifying it as the principal factor for spatial arrangement. Furthermore, the structural variations of ARGs were primarily driven by total organic carbon (TOC) (R[2] = 0.3988), temperature, oxidation-reduction potential (ORP) and NH4[+]-N. Our findings provided new insights into the optimization of substrate selection and ecological management to manage ARG enrichment, offering a promising strategy for aquatic ecological restoration and pollution control.},
}
@article {pmid39642832,
year = {2024},
author = {Fu, J and Chen, S and Tan, Y and Zou, K and Yu, X and Ji, L and Zhang, J and Xiao, X and Wang, W and Zhao, K and Zou, L},
title = {Inoculation of thermophilic bacteria from giant panda feces into cattle manure reduces gas emissions and decreases resistance gene prevalence in short-term composting.},
journal = {Journal of environmental management},
volume = {373},
number = {},
pages = {123601},
doi = {10.1016/j.jenvman.2024.123601},
pmid = {39642832},
issn = {1095-8630},
abstract = {Here, thermophilic bacteria (TB) with cellulose degradation functions were screened from composting panda feces and applied to cattle manure composting. TB (Aeribacillus pallidus G5 and Parageobacillus toebii G12) inoculation led to remarkable improvement of the compost temperature, prolonging of the thermophilic stage and shortening of the composting process, resulting in increased manure harmlessness (GI ≥ 70%), compost humification, and greenhouse gas emission reduction (14.19%-22.57%), compared with the control compost, within 15 days of composting. In particular, G5 inoculation reduced NH3 emissions by 41.97% relative to control composts over 15 days. G5 was capable of rapidly colonizing in the composts, and its inoculation immediately enriched the genera of Firmicutes, and simultaneously decreased the genera of Proteobacteria, contributing to the elimination of harmful microorganisms. Notably, this strain lacked antibiotic resistance genes, and the absolute abundances of resistance genes and mobile genetic genes (MGEs) decreased the most (by 80.84%). Metagenomic analysis revealed that enzymes capable of producing CO2, N2O, and NH3 were generally inhibited, while CO2 fixation and N2O and NH3 reduction enzymes were enriched in the G5 compost, since metagenome-assembled genomes of Proteobacteria harbored more key genes and enzymes in complete pathways for producing N2O, NH3, and CO2. Moreover, Proteobacteria, such as Pseudomonas and Halopseudomonas, were the main host of resistance genes and MGEs. Overall, the gas emission could be reduced, and more efficient control of resistance genes could be achieved by inhibited the abundance of Proteobacteria during composting. This study provides a safe and effective microbial agent (A. pallidus) for manure treatment.},
}
@article {pmid39642737,
year = {2024},
author = {Medriano, CA and Kim, S and Kim, LH and Bae, S},
title = {Chronic Exposure of Adult Zebrafish to Polyethylene and Polyester-based Microplastics: Metabolomic and Gut Microbiome Alterations Reflecting Dysbiosis and Resilience.},
journal = {Journal of hazardous materials},
volume = {484},
number = {},
pages = {136691},
doi = {10.1016/j.jhazmat.2024.136691},
pmid = {39642737},
issn = {1873-3336},
abstract = {The study explored the ecotoxicological effects of chronic exposure to microplastic (MP) on adult zebrafish, focusing on environmentally relevant concentrations of polyethylene (PE) beads and polyester (PES). High-throughput untargeted metabolomics via UPLC-QToF-MS and 16S metagenomics for gut microbiota analysis were used to assess ecotoxicity in zebrafish exposed to varying concentrations of PE and PES. The VIP (Variable Importance in Projection) scores indicated PE exposure primarily impacted phospholipids, ceramides, and nucleotide-related compounds, while PES exposure led to alterations in lipid-related compounds, chitin, and amino acid derivatives. From MSEA (Metabolite Set Enrichment Analysis) and Mummichog analyses, PE and PES significantly disrupted key metabolomic pathways associated with inflammation, immune responses, and apoptosis, including leukotriene and arachidonic acid metabolism and the formation of putative anti-inflammatory metabolites from EPA. PE caused physical disruption and inflammation of the epithelial barrier, whereas PES affected gut microbiota interactions, impairing digestion and metabolism. Although alpha diversity within the gut microbiome remained stable, beta diversity analysis revealed significant shifts in microbial composition and structure, suggesting a disruption of functional balance and an increased susceptibility to pathogens. Chronic PE and PES exposures induced shifts in the gut microbial community and interaction network with potential increases in pathogenic bacteria and alteration in commensal bacteria, demonstrating the microbiome's resilience and adaptability to stressors of MPs exposure. High-throughput metabolomics and 16S metagenomics revealed potential chronic diseases associated with inflammation, immune system disorders, metabolic dysfunction, and gut dysbiosis, highlighting the complex relationship between gut microbiome resilience and metabolic disruption under MP-induced stress, with significant ecological implications.},
}
@article {pmid39642431,
year = {2024},
author = {Bertini, F and Catania, V and Scirè Calabrisotto, L and Dara, M and Bisanti, L and La Corte, C and Staropoli, M and Piazzese, D and Parisi, MG and Parrinello, D and Cammarata, M},
title = {A multi-comprehensive approach to assess the responses of the Mediterranean mussel Mytilus galloprovincialis (Lamarck, 1919) to a simulation of a diesel-oil mixture spill.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {279},
number = {},
pages = {107188},
doi = {10.1016/j.aquatox.2024.107188},
pmid = {39642431},
issn = {1879-1514},
abstract = {Oil spills are a major cause of pollution impacting marine ecosystems. In this work, the effects of short-term exposure to three different concentrations of a hydrocarbon mixture (HC), that simulated the action of such an event, were investigated on Mytilus galloprovincialis specimens. Physiological effects were measured using a battery of biomarkers consisting of cellular activity (phagocytosis), immune-related enzymes, chaperonins (HSP70 and HSC70), and histomorphological alterations. Different concentrations of HC led to a significant decrease in phagocytosis, especially following high concentrations. Immune-related enzymes evaluated in hemolymph and digestive gland extract showed up-regulation, suggesting the activation of antioxidant, detoxicant, and inflammatory responses. Morphological alterations of digestive gland tubules were observed after exposure to the HC. HSP70 and HSC70 activity was up regulated following the treatments, indicating their involvement in maintaining organism homeostasis. In addition, the diversity and composition of hemolymph and digestive gland microbiota exposed to HC were analyzed by automated ribosomal intergenic spacer analysis (ARISA) and a Next Generation Sequencing (NGS) approach to evaluate the connection with hydrocarbon contamination. Metagenomic analysis revealed significant differences in the hemolymph and digestive gland microbiota composition between mussels exposed and unexposed to HC. Exposure to increasing HC concentrations had a positive effect on microbial diversity with clear adaptative responses, and an increase in the relative abundance of several known degrading bacterial genera, including Alcanivorax, Roseovarius, Pseudomonas, Vibrio, Oleibacter. These results show the utility of a multi-comprehensive approach to evaluating functional adaptation in terms of immunological dysfunctions and microbiota alteration in the sentinel organism M. galloprovincialis.},
}
@article {pmid39641861,
year = {2024},
author = {Leung, HKM and Lo, EKK and Chen, C and Zhang, F and Felicianna, and Ismaiah, MJ and El-Nezami, H},
title = {Probiotic Mixture Attenuates Colorectal Tumorigenesis in Murine AOM/DSS Model by Suppressing STAT3, Inducing Apoptotic p53 and Modulating Gut Microbiota.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {39641861},
issn = {1867-1314},
abstract = {Colorectal cancer (CRC) is one of the most common cancers worldwide. The standard CRC chemo drug, 5-Fluorouracil (5-FU), has a poor response rate and chemoresistance, prompting the need for a more effective and affordable treatment. In this study, we aimed to evaluate whether Prohep, a novel probiotic mixture, would alleviate azoxymethane/dextran sodium sulfate (AOM/DSS)-induced colorectal tumorigenesis and enhance 5-FU efficacy and its mechanism. Our results suggested that Prohep showed stronger anti-tumorigenesis effects than 5-FU alone or when combined in the AOM/DSS model. Prohep significantly reduced the total tumor count, total tumor size, caecum weight, colonic crypt depth, colonic inflammation, and collagen fibrosis. Prohep downregulated pro-inflammatory TNF-α and proliferative p-STAT3 and upregulated apoptotic p53. Metagenomics analysis indicated that Prohep-enriched Helicobacter ganmani, Desulfovibrio porci, Helicobacter hepaticus, and Candidatus Borkfalkia ceftriaxoniphila were inversely correlated to the total tumor count. In addition, Prohep-enriched Prevotella sp. PTAC and Desulfovibrio porci were negatively correlated to AOM/DSS enriched bacteria, while forming a co-existing community with other beneficial bacteria. From KEGG analysis, Prohep downregulated CRC-related pathways and enhanced pathways related to metabolites suppressing CRC like menaquinone, tetrapyrrole, aminolevulinic acid, and tetrahydrofolate. From Metacyc analysis, Prohep downregulated CRC-related peptidoglycan, LPS, and uric acid biosynthesis, and conversion. Prohep elevated the biosynthesis of the beneficial L-lysine, lipoic acid, pyrimidine, and palmitate. Prohep also elevated metabolic pathways related to energy utilization of lactic acid-producing bacteria (LAB) and acetate producers. Similarly, fecal acetate concentration was upregulated by Prohep. To sum up, Prohep demonstrated exceptional anti-tumorigenesis effects in the AOM/DSS model, which revealed its potential to develop into a novel CRC therapeutic in the future.},
}
@article {pmid39641605,
year = {2024},
author = {Bao, Z and Chen, B and Yu, K and Wei, Y and Liang, X and Yao, H and Liao, X and Xie, W and Yin, K},
title = {Microbiome dynamics and functional profiles in deep-sea wood-fall micro-ecosystem: insights into drive pattern of community assembly, biogeochemical processes, and lignocellulose degradation.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0216524},
doi = {10.1128/aem.02165-24},
pmid = {39641605},
issn = {1098-5336},
abstract = {Wood-fall micro-ecosystems contribute to biogeochemical processes in the oligotrophic deep ocean. However, the community assembly processes and biogeochemical functions of microbiomes in wood fall remain unclear. This study investigated the diversity, community structure, assembly processes, and functional profiles of bacteria and fungi in a deep-sea wood fall from the South China Sea using physicochemical indices, amplicon sequencing, and metagenomics. The results showed that distinct wood-fall contact surfaces exhibit habitat heterogeneity. The bacterial community of all contact surfaces and the fungal community of seawater contact surface (SWCS) were affected by homogeneous selection. In SWCS and transition region (TR), bacterial communities were influenced by dispersal limitation, whereas fungal communities were affected by homogenizing dispersal. The Venn diagram visualization revealed that the shared fungal community between SWCS and TR was dominated by Aspergillaceae. Additionally, the bacterial community demonstrated a higher genetic potential for sulfur, nitrogen, and methane metabolism than fungi. The sediment contact surface enriched modules were associated with dissimilatory sulfate reduction and methanogenesis, whereas the modules related to nitrate reduction exhibited enrichment characteristics in TR. Moreover, fungi showed a stronger potential for lignocellulase production compared to bacteria, with Microascaceae and Nectriaceae identified as potential contributors to lignocellulose degradation. These results indicate that environmental filtering and organism exchange levels regulated the microbial community assembly of wood fall. The biogeochemical cycling of sulfur, nitrogen, and methane was mainly driven by the bacterial community. Nevertheless, the terrestrial fungi Microascaceae and Nectriaceae might degrade lignocellulose via the combined action of multiple lignocellulases.IMPORTANCEThe presence and activity of microbial communities may play a crucial role in the biogeochemical cycle of deep-sea wood-fall micro-ecosystems. Previous studies on wood falls have focused on the microbiome diversity, community composition, and environmental impact, while few have investigated wood-fall micro-ecosystems by distinguishing among distinct contact surfaces. Our study investigated the microbiome dynamics and functional profiles of bacteria and fungi among distinct wood-fall contact surfaces. We found that the microbiome community assembly was regulated by environmental filtering and organism exchange levels. Bacteria drive the biogeochemical cycling of sulfur, nitrogen, and methane in wood fall through diverse metabolic pathways, whereas fungi are crucial for lignocellulose degradation. Ultimately, this study provides new insights into the driving pattern of community assembly, biogeochemical processes, and lignocellulose degradation in the microbiomes of deep-sea wood-fall micro-ecosystems, enhancing our comprehension of the ecological impacts of organic falls on deep-sea oligotrophic environments.},
}
@article {pmid39641169,
year = {2024},
author = {Yang, J and Lei, OK and Bhute, S and Kris-Etherton, PM and Lichtenstein, AH and Matthan, NR and Petersen, KS and Sabaté, J and Reboussin, DM and Lovato, L and Vitolins, MZ and Rajaram, S and Jacobs, JP and Huang, J and Taw, M and Yang, S and Li, Z},
title = {Impact of daily avocado consumption on gut microbiota in adults with abdominal obesity: an ancillary study of HAT, a randomized controlled trial.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo03806a},
pmid = {39641169},
issn = {2042-650X},
abstract = {Objectives: This study aimed to investigate short-term and long-term impact of avocado consumption without caloric restriction on the gut microbiota of free-living adults with abdominal obesity. Methods: The Habitual Diet and Avocado Trial (HAT) was a 26-week, multi-center, randomized, controlled trial involving 1008 individuals with abdominal obesity. Participants were randomly assigned to the Avocado Supplemented Diet Group (AVO), receiving one avocado per day, or the Habitual Diet group (HAB), maintaining their usual dietary habits. Fecal samples were collected at baseline, week 4 and week 26 from a subset of participants recruited at a University of California Los Angeles site (n = 230). Fecal microbiota was assessed with shotgun metagenomics sequencing. Alpha diversity was assessed using the Chao1 and Shannon indices; beta diversity was assessed using Bray-Curtis dissimilarity with significance determined by repeated measures permutational multivariat analysis of variance. Potential association of intervention at week 4 and 26 with alpha diversity, species and metabolic pathways was examined using linear mixed effect models. Results: Compared to the HAB group, the AVO group had higher alpha diversity by 4 weeks, which persisted through the 26-week study period. Exploratory analysis based on healthy eating index-2015 (HEI-2015) indicated that participants with a low HEI score at baseline (≤52.7), had an increase in alpha diversity in the AVO group vs. HAB group. The AVO group had a significant change in beta diversity at week 26 compared to the HAB group. At the species level, the AVO group had significantly increased Faecalibacterium prausnitzii and Bacterium AF16_15 at week 26 compared to the HAB group. Functional analysis showed no significant difference in metabolic pathways between the HAB and AVO groups. Conclusions: Our findings document a potentially favorable effect of avocados on gut microbiota diversity. The prebiotic potential of avocados is more pronounced in individuals with a low diet quality score. This trial is registered at clinicaltrials.gov as NCT03528031 (https://clinicaltrials.gov/study/NCT03528031).},
}
@article {pmid39641037,
year = {2024},
author = {Wang, F and Zhan, Q and Yu, A and Chen, H and Zhang, Y and Yang, Q and Qu, T},
title = {Mediastinitis caused by Mycoplasma hominis in immunocompetent patients: A case series report and literature review.},
journal = {Heliyon},
volume = {10},
number = {22},
pages = {e39763},
pmid = {39641037},
issn = {2405-8440},
abstract = {BACKGROUND: Mycoplasma hominis, a commensal organism, is potentially pathogenic; its role in postoperative infections might be underestimated in cardiac surgery.<br><br>RESULTS: We reported two cases of postoperative M. hominis mediastinitis in immunocompetent patients with a DeBakey grade I aortic dissecting aneurysm and reviewed 10 other cases previously described. Among the 10 reviewed cases and our two cases, 11 patients were men (median age, 59 years; median onset of clinical symptoms time, 14.5&#xa0;d after surgery; and mean peak of temperature, 38.5&#xa0;&#xb1;&#xa0;0.8&#xa0;&#xb0;C). In our reports, two patients underwent sternotomy site reopening and debridement before diagnosis was confirmed. Diagnosis was confirmed by prolonged culture and by performing metagenomic next-generation sequencing directly using the clinical samples. M. hominis was difficult to cover with initial empirical antibiotic therapy; the patient in this study showed complete improvement with long-term antimicrobial therapy. The targeted treatment duration for surviving patients among the reviewed cases ranged from three weeks to 16 months.<br><br>CONCLUSIONS: The diagnosis of extragenital M. hominis infections is difficult. Therefore, the role of M. hominis as a cause of postoperative infections during cardiac surgery should be considered. Diagnosis requires molecular techniques to complement culture.},
}
@article {pmid39640900,
year = {2024},
author = {Pahirah, N and Narkwichean, A and Taweechotipatr, M and Wannaiampikul, S and Duang-Udom, C and Laosooksathit, W},
title = {Comparison of Gut Microbiomes Between Neonates Born by Cesarean Section and Vaginal Delivery: Prospective Observational Study.},
journal = {BioMed research international},
volume = {2024},
number = {},
pages = {8302361},
pmid = {39640900},
issn = {2314-6141},
mesh = {Humans ; *Cesarean Section ; *Gastrointestinal Microbiome ; Infant, Newborn ; Female ; Prospective Studies ; *Delivery, Obstetric ; Pregnancy ; *RNA, Ribosomal, 16S/genetics ; Male ; Feces/microbiology ; Thailand ; Bifidobacterium ; },
abstract = {Background: Balanced diversity and abundance of gut microbiome play important roles in human health, including neonatal health. Though not established, there is evidence that the delivery route could alter the diversity of neonatal gut microbiomes. Objective: The objective of the study was to investigate the differences in the gut microbiomes of neonates delivered via cesarean section compared to those born by vaginal delivery and to identify the predominant microbial taxa present in each group. Study Design: A prospective observational study of 281 healthy neonates born between February 2021 and April 2023 at Her Royal Highness Maha Chakri Sirindhorn Medical Center, Srinakharinwirot University, Thailand, was performed. The study population was divided into two groups: 139 neonates born via vaginal delivery and 141 neonates born via cesarean section. The microbiota composition of each neonate's fecal sample was identified by using 16S ribosomal ribonucleic acid metagenomic sequencing. Results: Neonates delivered vaginally exhibited a gut microbiome with higher abundance and diversity than those delivered by cesarean delivery. Bifidobacterium was the dominant genus in both groups. Bifidobacterium breve was the dominant species and was significantly higher in cesarean-delivered neonates compared to those delivered vaginally (24.0% and 9.2%, respectively) (p < 0.001). However, the taxonomy of only 89 (64.0%) and 44 (31.43%) fecal samples could be identified from the vaginal and cesarean delivery groups, respectively. Conclusion: Route of delivery is associated with neonatal gut microbiome abundance and diversity. Neonates delivered via vaginal delivery exhibited higher diversity but lower abundance of the dominant species in the gut microbiome. Trial Registration: Thai Clinical Trials Registry identifier: TCTR20221024003.},
}
@article {pmid39639912,
year = {2024},
author = {Balingit, AK and Grande, PG and Nicolasora, AD and Polotan, FG and Pantoni, RA and Abulencia, MF and Chu, MYJ and Rivera, N and Oblepias, MS and Garcia, J},
title = {Clinical presentation and molecular diagnosis of a possible Mpox virus and Varicella zoster virus co-infection in an adult immunocompetent Filipino: a case report.},
journal = {Frontiers in public health},
volume = {12},
number = {},
pages = {1387636},
pmid = {39639912},
issn = {2296-2565},
mesh = {Humans ; Adult ; Female ; Philippines ; *Coinfection/diagnosis ; *Herpesvirus 3, Human/isolation &amp; purification/genetics ; Varicella Zoster Virus Infection/diagnosis/complications ; Chickenpox/diagnosis ; Switzerland ; Travel ; },
abstract = {We report the first travel-related case of a possible Mpox-Varicella zoster virus (VZV) co-infection in the Philippines, a country that is endemic for Varicella but non-endemic for Mpox. A 29-year-old Filipino, female, with a travel history to Switzerland and with no prior history of VZV infection sought consultation due to rashes. She presented with multiple papular, pustular, and vesicular skin lesions, some with umbilication and with irregular borders, on the face, neck, trunk, inguinal area, upper extremities, and right leg. She also had bilateral submandibular and post-auricular lymphadenopathies. Tzanck smear exhibited viral cytopathic effects. She tested positive for Mpox infection (Clade II) and Varicella infection via quantitative real-time polymerase chain reaction (qPCR) tests but with a high CT value obtained from the Mpox PCR. Shotgun metagenomic sequencing (mNGS) successfully recovered sequences from the Varicella zoster virus which corroborated with the high viral load detected using qPCR. In contrast, shotgun mNGS was not able to generate a Mpox consensus sequence due to very few reads mapped to the Mpox virus reference sequence, which raised the question if there was the presence of a true Mpox-Varicella co-infection in our patient. Nevertheless, systemic and topical acyclovir was given to the patient. She was discharged and continued home isolation for 30 days from the rash onset. Strategies have been formed by the country's healthcare facilities to properly identify Mpox infection. However, Mpox co-infection with other viral diseases presented a challenge in the proper diagnosis of our patient. This prompted a high index of suspicion and the usage of suitable diagnostic tests. With proper clinical evaluation and utilization of appropriate diagnostic tests, we were able to diagnose the first Filipino patient with a possible Mpox and Varicella zoster virus co-infection.},
}
@article {pmid39639673,
year = {2024},
author = {Wynne, JW and English, CJ and Vannetti, SM and Rigby, M and Quezada-Rodriguez, PR and Knüsel, R and Huynh, C and Schmidt-Posthaus, H},
title = {18S rRNA Metagenomic Analysis of Nodular Gill Disease in Swiss Rainbow Trout (Oncorhynchus mykiss).},
journal = {Journal of fish diseases},
volume = {},
number = {},
pages = {e14061},
doi = {10.1111/jfd.14061},
pmid = {39639673},
issn = {1365-2761},
support = {//CSIRO Julius Career Award/ ; //European Association of Fish Pathologists Small Grant Scheme/ ; //Swiss Food Safety and Veterinary Office/ ; //the Swiss Food Safety and Veterinary Office/ ; },
abstract = {Nodular gill disease (NGD) is a serious proliferative gill condition that affects farmed salmonids, particularly in Europe. While the cause of NGD remains unknown (and maybe multifactorial), various amoebae are often isolated from the gills of affected fish and can in some cases be seen associated with lesions by histopathology. The present study aimed to quantify the abundance of different amoeba species directly from the gills of rainbow trout affected by NGD and healthy controls. An 18S rRNA amplicon metagenomic approach was employed to profile the diversity and abundance of micro-eukaryotes (including amoebae) while suppressing the amplification of host DNA using a salmonid-specific C3 spacer blocking primer. The 18S rRNA metagenomics approach identified a diversity of micro-eukaryotes on the gills of rainbow trout, including the phylum's Amoebozoa, Diatomea, Platyhelminthes and Ciliophora. Rainbow trout clinically affected by NGD had a significantly higher abundance of a specific sequence (zOTU2) classified as Vannella sp. compared to healthy controls. A quantitative PCR assay was then developed and validated which accurately quantified the abundance of this Vannella sp. sequence from a NGD outbreak in a Swiss rainbow trout farm. Additional PCR and Sanger sequencing analysis of the zOTU2 sequence demonstrated that this sequence is most likely derived from Vannella mustalahtiana. Our study highlights the potential role of Vannella mustalahtiana in NGD in Switzerland and further describes a specific and validated diagnostic PCR assay for accurate detection of this Vannella species.},
}
@article {pmid39639495,
year = {2024},
author = {Alanzi, AR},
title = {Exploring Microbial Dark Matter for the Discovery of Novel Natural Products: Characteristics, Abundance Challenges and Methods.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {},
doi = {10.4014/jmb.2407.07064},
pmid = {39639495},
issn = {1738-8872},
abstract = {The objective of this review is to investigate microbial dark matter (MDM) with a focus on its potential for discovering novel natural products. This first part will examine the characteristics and abundance of these previously unexplored microbial communities, as well as the challenges faced in identifying and harnessing their unique biochemical properties and novel methods in this field. MDMs are thought to hold great potential for the discovery of novel natural products, which could have significant applications in medicine, agriculture, and industry. In recent years, there has been a growing interest in exploring microbial dark matter to unlock its potential. In fact, developments in genome-sequencing technologies and sophisticated phylogenetic procedures and metagenomic techniques have contributed to drastically make important changes in our sights on the diversity of microbial life, including the very outline of the tree of life. This has led to the development of novel technologies and methodologies for studying these elusive microorganisms, such as single-cell genomics, metagenomics, and culturomics. These approaches enable researchers to isolate and analyze individual microbial cells, as well as entire communities, providing insights into their genetic and metabolic potential. By delving into the microbial dark matter, scientists hope to uncover new compounds and biotechnological advancements that could have far-reaching impacts on various fields.},
}
@article {pmid39639405,
year = {2024},
author = {Nechalová, L and Bielik, V and Hric, I and Babicová, M and Baranovičová, E and Grendár, M and Koška, J and Penesová, A},
title = {Gut microbiota and metabolic responses to a 12-week caloric restriction combined with strength and HIIT training in patients with obesity: a randomized trial.},
journal = {BMC sports science, medicine &amp; rehabilitation},
volume = {16},
number = {1},
pages = {239},
pmid = {39639405},
issn = {2052-1847},
support = {UK/213/2022//Grant mlad&#xfd;ch UK/ ; APVV-17-0099//Agent&#xfa;ra na Podporu V&#xfd;skumu a V&#xfd;voja/ ; VEGA 1/0260/21//Vedeck&#xe1; Grantov&#xe1; Agent&#xfa;ra M&#x160;VVa&#x160; SR a SAV/ ; VEGA 2/0129/20//Vedeck&#xe1; Grantov&#xe1; Agent&#xfa;ra M&#x160;VVa&#x160; SR a SAV/ ; },
abstract = {BACKGROUND: Nowadays, obesity has become a major health issue. In addition to negatively affecting body composition and metabolic health, recent evidence shows unfavorable shifts in gut microbiota in individuals with obesity. However, the effects of weight loss on gut microbes and metabolites remain controversial. Therefore, the purpose of this study was to investigate the effects of a 12-week program on gut microbiota and metabolic health in patients with obesity.<br><br>METHODS: We conducted a controlled trial in 23 male and female patients with obesity. Twelve participants completed a 12-week program of caloric restriction combined with strength and HIIT training (INT, pre-BMI 37.33&#x2009;&#xb1;&#x2009;6.57&#xa0;kg/m[2]), and eleven participants were designated as non-intervention controls (pre-BMI 38.65&#x2009;&#xb1;&#x2009;8.07&#xa0;kg/m[2]). Metagenomic sequencing of the V3-V4 region of the 16S rDNA gene from fecal samples allowed for gut microbiota classification. Nuclear magnetic resonance spectroscopy characterized selected serum and fecal metabolite concentrations.<br><br>RESULTS: Within INT, we observed a significant improvement in body composition; a significant decrease in liver enzymes (AST, ALT, and GMT); a significant increase in the relative abundance of the commensal bacteria (e.g., Akkermansia muciniphila,&#xa0;Parabacteroides merdae, and Phocaeicola vulgatus); and a significant decrease in the relative abundance of SCFA-producing bacteria (e.g., the genera Butyrivibrio, Coprococcus, and Blautia). In addition, significant correlations were found between gut microbes, body composition, metabolic health biomarkers, and SCFAs. Notably, the Random Forest Machine Learning analysis identified predictors (Butyrivibrio fibrisolvens, Blautia caecimuris, Coprococcus comes, and waist circumference) with a moderate ability to discriminate between INT subjects pre- and post-intervention.<br><br>CONCLUSIONS: Our results indicate that a 12-week caloric restriction combined with strength and HIIT training positively influences body composition, metabolic health biomarkers, gut microbiota, and microbial metabolites, demonstrating significant correlations among these variables. We observed a significant increase in the relative abundance of bacteria linked to obesity, e.g., Akkermansia muciniphila. Additionally, our study contributes to the ongoing debate about the role of SCFAs in obesity, as we observed a significant decrease in SCFA producers after a 12-week program.<br><br>TRIAL REGISTRATION: The trial was registered on [05/12/2014] with ClinicalTrials.gov (No: NCT02325804).},
}
@article {pmid39639355,
year = {2024},
author = {Benga, L and Rehm, A and Gougoula, C and Westhoff, P and Wachtmeister, T and Benten, WPM and Engelhardt, E and Weber, APM and Köhrer, K and Sager, M and Janssen, S},
title = {The host genotype actively shapes its microbiome across generations in laboratory mice.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {256},
pmid = {39639355},
issn = {2049-2618},
mesh = {Animals ; Mice ; Female ; *Genotype ; *Mice, Inbred BALB C ; *Mice, Inbred C57BL ; *Microbiota ; Male ; Maternal Inheritance ; Embryo, Mammalian/microbiology ; Host Microbial Interactions ; Pregnancy ; },
abstract = {BACKGROUND: The microbiome greatly affects health and wellbeing. Evolutionarily, it is doubtful that a host would rely on chance alone to pass on microbial colonization to its offspring. However, the literature currently offers only limited evidence regarding two alternative hypotheses: active microbial shaping by host genetic factors or transmission of a microbial maternal legacy.<br><br>RESULTS: To further dissect the influence of host genetics and maternal inheritance, we collected two-cell stage embryos from two representative wild types, C57BL6/J and BALB/c, and transferred a mixture of both genotype embryos into hybrid recipient mice to be inoculated by an identical microbiome at birth.<br><br>CONCLUSIONS: Observing the offspring for six generations unequivocally emphasizes the impact of host genetic factors over maternal legacy in constant environments, akin to murine laboratory experiments. Interestingly, maternal legacy solely controlled the microbiome in the first offspring generation. However, current evidence supporting maternal legacy has not extended beyond this initial generation, resolving the aforementioned debate. Video Abstract.},
}
@article {pmid39639243,
year = {2024},
author = {Li, J and Pan, D and Guo, Y and Zhang, B and Lu, X and Deng, C and Xu, F and Lv, Z and Chen, Q and Zheng, Y and Nong, S and Su, L and Qin, R and Jiang, F and Gai, W and Qin, G},
title = {Clinical application value of simultaneous plasma and bronchoalveolar lavage fluid metagenomic next generation sequencing in patients with pneumonia-derived sepsis.},
journal = {BMC infectious diseases},
volume = {24},
number = {1},
pages = {1393},
pmid = {39639243},
issn = {1471-2334},
mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; Female ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing ; *Sepsis/diagnosis/microbiology/mortality ; Middle Aged ; Aged ; *Metagenomics/methods ; Pneumonia/microbiology/diagnosis ; Intensive Care Units ; Prognosis ; Bacteria/isolation &amp; purification/genetics/classification ; },
abstract = {BACKGROUND: Despite the increasing use of metagenomic next-generation sequencing (mNGS) in sepsis, identifying clinically relevant pathogens remains challenging. This study was aimed to evaluate the clinical utility of simultaneous plasma and bronchoalveolar lavage fluid (BALF) detection using mNGS.<br><br>METHODS: This retrospective study enrolled 95 patients with pneumonia-derived sepsis (PDS) admitted to the intensive care unit (ICU) between October 2021 and January 2023. Patients were divided into two groups: mNGS group (n&#x2009;=&#x2009;60) and the non-mNGS group (n&#x2009;=&#x2009;35), based on whether simultaneous plasma and BALF mNGS were conducted. All patients underwent conventional microbiological tests (CMT), including bacterial/fungal culture of peripheral blood and BALF, as well as sputum culture, detection of 1, 3-beta-D- glucan in BALF and RT-PCR testing. The clinical data of the enrolled patients were collected, and the detection performance and prognosis of plasma mNGS, BALF mNGS and CMT were compared.<br><br>RESULTS: The mNGS group exhibited a lower mortality rate than the non-mNGS group (35.0% vs. 57.1%, P&#x2009;=&#x2009;0.034). Simultaneous detection in dual-sample resulted in a higher proportion of microorganisms identified as definite causes of sepsis alert compared to detection in either plasma or BALF alone (55.6% vs. 20.8% vs. 18.8%, P<0.001). Acinetobacter baumannii, Stenotrophomonas maltophilia, Candida albicans, and human mastadenovirus B were the primary strains responsible for infections in PDS patients. Patients with lower white blood cells and neutrophil indices had a greater consistency in dual-sample mNGS. Patients in the mNGS group had more antibiotic adjustments compared to the non-mNGS group (85.71% vs. 33.33%, P<0.001). The percentage of neutrophils was a risk factor for mortality in PDS patients (P&#x2009;=&#x2009;0.002).<br><br>CONCLUSION: Dual sample mNGS has the advantage of detecting and determining the pathogenicity of more pathogens and has the potential to improve the prognosis of patients with PDS.},
}
@article {pmid39639163,
year = {2024},
author = {Taglialegna, A},
title = {Metagenomics for drug discovery.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39639163},
issn = {1740-1534},
}
@article {pmid39639104,
year = {2024},
author = {Knuth, MM and Campos, CV and Smith, K and Hutchins, EK and Lewis, S and York, M and Coghill, LM and Franklin, C and MacFarlane, AJ and Ericsson, AC and Magnuson, T and Ideraabdullah, F},
title = {Timing of standard chow exposure determines the variability of mouse phenotypic outcomes and gut microbiota profile.},
journal = {Lab animal},
volume = {},
number = {},
pages = {},
pmid = {39639104},
issn = {1548-4475},
abstract = {Standard chow diets influence reproducibility in animal model experiments because chows have different nutrient compositions, which can independently influence phenotypes. However, there is little evidence of the role of timing in the extent of variability caused by chow exposure. Here we measured the impact of different diets (5V5M, 5V0G, 2920X and 5058) and timing of exposure (adult exposure (AE), lifetime exposure (LE) and developmental exposure (DE)) on growth and development, metabolic health indicators and gut bacterial microbiota profiles across genetically identical C57BL/6J mice. Diet drove differences in macro- and micronutrient intake for all exposure models. AE had no effect on phenotypic outcomes. However, LE mice exhibited significant sex-dependent diet effects on growth, body weight and body composition. LE effects were mostly absent in the DE model, where mice were exposed to chow differences only from conception to weaning. Both AE and LE models exhibited similar diet-driven beta diversity profiles for the gut bacterial microbiota, with 5058 diet driving the most distinct profile. However, compared with AE, LE effects on beta diversity were sex dependent, and LE mice exhibited nine times more differentially abundant bacterial genera, the majority of which were inversely affected by 2920X and 5058 diets. Our findings demonstrate that LE to different chow diets has the greatest impact on the reproducibility of several experimental measures commonly used in preclinical mouse model studies. Importantly, weaning mice from different diets onto the same diet for maturation may be an effective way to reduce unwanted phenotypic variability among experimental models.},
}
@article {pmid39638008,
year = {2024},
author = {Liu, LY and Dang, CC and Tan, X and Liu, BF and Lu, Y and Zhao, ZC and Wang, X and Wang, XW and Xing, DF and Ren, NQ and Xie, GJ},
title = {Thermophilic anaerobic ethane oxidation coupled with selenate and selenite reduction.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131934},
doi = {10.1016/j.biortech.2024.131934},
pmid = {39638008},
issn = {1873-2976},
abstract = {Anaerobic microorganisms are critical in regulating ethane in geothermal environments, where selenate and selenite are common contaminants. Although coupling ethane oxidation with selenate reduction has been demonstrated as feasible, such processes remain poorly explored in geothermal environments. This study addressed this gap by successfully enriching thermophilic anaerobic cultures capable of coupling ethane oxidation with selenate/selenite reduction, achieving selenate and selenite removal rate of 2.7 mg Se/L/d and 2.1 mg Se/L/d, respectively. Metagenomic analysis revealed a novel genus 'Candidatus Ethanivorans selenatireducens', which accounted for 16.0 % and 32.6 % of microbial communities in selenate- and selenite-dependent systems, respectively. This microorganism encoded pathways for anaerobic ethane oxidation via fumarate addition and genes required for the sequential reduction of selenate to elemental selenium. These findings unveiled a novel microbial mechanism linking ethane oxidation and selenate reduction in geothermal systems, providing new insights into the biogeochemical interaction between carbon and selenium in thermophilic environments.},
}
@article {pmid39637857,
year = {2024},
author = {Vaher, K and Cabez, MB and Parga, PL and Binkowska, J and van Beveren, GJ and Odendaal, ML and Sullivan, G and Stoye, DQ and Corrigan, A and Quigley, AJ and Thrippleton, MJ and Bastin, ME and Bogaert, D and Boardman, JP},
title = {The neonatal gut microbiota: A role in the encephalopathy of prematurity.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {101845},
doi = {10.1016/j.xcrm.2024.101845},
pmid = {39637857},
issn = {2666-3791},
abstract = {Preterm birth correlates with brain dysmaturation and neurocognitive impairment. The gut microbiome associates with behavioral outcomes in typical development, but its relationship with neurodevelopment in preterm infants is unknown. We characterize fecal microbiome in a cohort of 147 neonates enriched for very preterm birth using 16S-based and shotgun metagenomic sequencing. Delivery mode strongly correlates with the preterm microbiome shortly after birth. Low birth gestational age, infant sex assigned at birth, and antibiotics associate with microbiome composition at neonatal intensive care unit discharge. We integrate these data with term-equivalent structural and diffusion brain MRI. Bacterial community composition associates with MRI features of encephalopathy of prematurity. Particularly, abundances of Escherichia coli and Klebsiella spp. correlate with microstructural parameters in deep and cortical gray matter. Metagenome functional capacity analyses suggest that these bacteria may interact with brain microstructure via tryptophan and propionate metabolism. This study indicates that the gut microbiome associates with brain development following preterm birth.},
}
@article {pmid39637856,
year = {2024},
author = {Caty, SN and Alvarez-Buylla, A and Vasek, C and Tapia, EE and Martin, NA and McLaughlin, T and Golde, CL and Weber, PK and Mayali, X and Coloma, LA and Morris, MM and O'Connell, LA},
title = {Alkaloids are associated with increased microbial diversity and metabolic function in poison frogs.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.10.069},
pmid = {39637856},
issn = {1879-0445},
abstract = {Shifts in host-associated microbiomes can impact both host and microbes.[1][,][2][,][3][,][4][,][5][,][6] It is of interest to understand how perturbations, like the introduction of exogenous chemicals,[7][,][8][,][9][,][10][,][11][,][12][,][13] impact microbiomes. In poison frogs (family Dendrobatidae), the skin microbiome is exposed to alkaloids that the frogs sequester for defense.[14][,][15][,][16][,][17][,][18][,][19] These alkaloids are antimicrobial[20][,][21][,][22]; however, their effect on the frogs' skin microbiome is unknown. To test this, we characterized microbial communities from field-collected dendrobatid frogs. Then, we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of two frog species with contrasting alkaloid loads in nature. In both datasets, we found that alkaloid-exposed microbiomes were more phylogenetically diverse, with an increase in diversity among rare taxa. To better understand the isolate-specific response to alkaloids, we cultured microbial isolates from poison frog skin and found that many isolates exhibited enhanced growth or were not impacted by the addition of DHQ. To further explore the microbial response to alkaloids, we sequenced the metagenomes from high- and low-alkaloid frogs and observed a greater diversity of genes associated with nitrogen and carbon metabolism in high-alkaloid frogs. From these data, we hypothesized that some strains may metabolize the alkaloids. We used stable isotope tracing coupled to nanoSIMS (nanoscale secondary ion mass spectrometry), which supported the idea that some of these isolates are able to metabolize DHQ. Together, these data suggest that poison frog alkaloids open new niches for skin-associated microbes with specific adaptations, such as alkaloid metabolism, that enable survival in this environment.},
}
@article {pmid39637791,
year = {2024},
author = {Xue, W and Zhang, S and Younas, F and Ma, R and Yu, X and Li, J and Wu, X and Liu, W and Duan, H and Wang, K and Cui, X and Cao, X and Cui, Z},
title = {The combined effects of tetracycline and glyphosate on growth and rhizosphere bacteria community in hulless barley over the whole growth period.},
journal = {Journal of hazardous materials},
volume = {484},
number = {},
pages = {136706},
doi = {10.1016/j.jhazmat.2024.136706},
pmid = {39637791},
issn = {1873-3336},
abstract = {The toxic effects of tetracycline and glyphosate on hulless barley and its environment, as well as their interrelationship, remain poorly understood. The present study aimed to identify biomarkers reflective of tetracycline and glyphosate toxicity, examine root damage and rhizosphere bacterial communities throughout the growth cycle, and assess the final grain quality. Results indicated that the hydrogen peroxide (H2O2) content in the underground parts of barley could serve as a sensitive biomarker for detecting tetracycline and glyphosate toxicity in barley. In addition, a synergistic effect between 5 mg/kg tetracycline and 5 mg/kg glyphosate was observed at the tillering stage, which not only induced H2O2 accumulation across all growth stages but also ultimately reduced seed quality. During the tillering phase, Proteobacteria dominanted, while Actinobacteria showed greater relative abundance during the jointing stage.By the ripening stage, Acidobacteria predominantly colonized the associated soils. Importantly, the study further identified metagenome-assembled genomes containing cytochrome P450 fragments capable of metabolizing these compounds. This study provides novel insights into the transformation of co-contaminants and the adaptive responses of rhizobacteria to tetracycline and glyphosate exposure, offering valuable information for agricultural practices.},
}
@article {pmid39637780,
year = {2024},
author = {Huang, C and Cui, M and Li, T and Zheng, C and Qiu, M and Shan, M and Li, B and Zhang, L and Yu, Y and Fang, H},
title = {Migration of fungicides, antibiotics and resistome in the soil-lettuce system.},
journal = {Journal of hazardous materials},
volume = {484},
number = {},
pages = {136725},
doi = {10.1016/j.jhazmat.2024.136725},
pmid = {39637780},
issn = {1873-3336},
abstract = {The emergence and spread of antibiotic resistance genes (ARGs) have become a serious issue in global agricultural production. However, understanding how these ARGs spread across different spatial scales, especially when exposed to both pesticides and antibiotics, has remained a challenge. Here, metagenomic assembly and binning methodologies were used to determine the spread pathway of ARGs in the soil-lettuce system under individual and combined exposure of fungicides (carbendazim and pyraclostrobin) and antibiotics (chlortetracycline and ciprofloxacin). These agrochemicals not only facilitated the spread of ARGs from soil to lettuce but also significantly elevated the risk of developing multi-antibiotic resistance among bacteria, especially to some antibiotic types (i.e. sulfonamide, aminoglycoside, quinolone, and tetracycline). ARGs could be migrated through distinct pathways, including both vertical and horizontal gene transfer, with plasmids playing a crucial role in facilitating the horizontal gene transfer. These transfer pathways have enabled key pathogenic bacteria belonging to the genera Acinetobacter, Pseudomonas, and Pantoea to acquire resistance and remain recalcitrant, posing the potential risk to crop health and food safety. In summary, our findings highlighted that fungicide and antibiotic could drive upward migration of ARGs in the soil-lettuce system and reduced the quality safety of agricultural products.},
}
@article {pmid39637691,
year = {2024},
author = {Yan, J and Zhang, X and Shi, X and Wu, J and Zhou, Z and Tang, Y and Bao, Z and Luo, N and Zhang, D and Chen, J and Zhang, H},
title = {Metagenomic insights into the rapid recovery mechanisms of prokaryotic community and spread of antibiotic resistance genes after seawater disinfection.},
journal = {Water research},
volume = {271},
number = {},
pages = {122887},
doi = {10.1016/j.watres.2024.122887},
pmid = {39637691},
issn = {1879-2448},
abstract = {Disinfectants, such as bleaching powder, are widely employed in marine aquaculture worldwide to control the bacterial pathogens and eliminate antibiotic resistance genes (ARGs). Nevertheless, the rapid recovery of prokaryotic community compositions (PCCs) after disinfection may significantly influence the overall efficacy of disinfection. Presently, little is known about the rapid recovery mechanisms of PCCs and its impact on the removal of ARGs in seawater. In this study, 16S rRNA gene sequencing and metagenomic analysis were used to address the above concerns through simulating the disinfection process in aquaculture. The results showed that recovery of PCCs began within 16 h. The underlying mechanisms of the rapid recovery of PCCs were the synergistic interactions between microbes and the residues of disinfection-resistant bacteria (DRB). Disinfection resistance genes (DRGs) related to efflux pump serve as the primary molecular foundation providing DRB to resist disinfection. Among the 78 annotated ARGs, only 10 ARGs exhibited a significant decrease (P < 0.05) after 72 h, implying the ineffective removal of ARGs by bleaching powder. Furthermore, bacterial co-resistance to disinfectants and antibiotics was observed. Genome analysis of two highly resistant DRB from Pseudomonadaceae revealed that both DRB carried 16 DRGs, aiding the recovery of PCCs and the spread of ARGs. These findings provide novel insights in the mechanisms of the rapid recovery of PCCs and bacterial co-resistance to disinfectants and antibiotics, which can be crucial for the management of pathogens and antibiotic resistance in seawater.},
}
@article {pmid39637538,
year = {2024},
author = {Gu, T and Ni, Z and Zhao, Q and Li, R and Qiu, R and Zhang, WX},
title = {Control of arsenic methylation in paddy soils by iron nanoparticles.},
journal = {The Science of the total environment},
volume = {957},
number = {},
pages = {177828},
doi = {10.1016/j.scitotenv.2024.177828},
pmid = {39637538},
issn = {1879-1026},
abstract = {Rice, as the most essential food grain, is frequently exposed to high concentrations of arsenic. Among the arsenic species, dimethylarsenate (DMAs(V)) is preferentially translocated from paddy soils to rice grains, posing serious threats to food safety and yield. Herein, we report an efficient strategy for DMAs(V) mitigation in paddy soils with nanoscale Zero-Valent Iron (nZVI). Species and concentrations of arsenic in paddy porewater were monitored during a 28-d soil-water incubation. Effects of nZVI dose towards microbial sulfate reduction and methane generation potential in paddy soils, which are crucial for arsenic methylation and demethylation, were analyzed via metagenomic sequencing. Results demonstrated that the maximal DMAs(V) concentration in paddy porewater decreased from 0.37 to 0.04 μM in arsenic-contaminated paddy soils with nZVI dose increasing from 0 to 5.0 g/kg. Accordingly, the maximal concentration of inorganic arsenite (iAs(III)), which is the precursor of DMAs(V), decreased from 1.39 to 0.23 μM. Furthermore, the application of nZVI reshaped the structure of microbial community in paddy soils. Specifically, the relative abundance of δ-proteobacteria involved in sulfate reduction, which is crucial for iAs(III) methylation, waned from 7.62 % to 3.17 %, while that of Methanomicrobia for DMAs(V) demethylation and methanogenesis proliferated from 7.03 % to 13.62 %, with nZVI dose increasing from 0 to 5.0 g/kg. Via simultaneous inhibition of DMAs(V) formation and acceleration of DMAs(V) transformation, nZVI efficiently controls the accumulation of DMAs(V) in paddy porewater. In conclusion, these findings prove the efficient performance for DMAs(V) mitigation with nZVI and uncover its underlying mechanisms.},
}
@article {pmid39637512,
year = {2024},
author = {Wilkie, I and Orellana, LH},
title = {Elusive marine Verrucomicrobiota: Seasonally abundant members of the novel genera Seribacter and Chordibacter specialize in degrading sulfated glycans.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {1},
pages = {126562},
doi = {10.1016/j.syapm.2024.126562},
pmid = {39637512},
issn = {1618-0984},
abstract = {Members of the phylum Verrucomicrobiota play a significant role in various ecosystems, yet they are underrepresented in databases due to their comparatively lower abundance and isolation challenges. The use of cultivation-independent approaches has unveiled their hidden diversity and specialized metabolic capabilities, yet many of these populations remain uncharacterized. In this study, we focus on members of the family MB11C04 associated with North Sea spring blooms. Our analyses revealed recurrent MB11C04 populations with increased abundance in the late stages of spring blooms over ten-years. By examining their genomic content, we identified specialized genetic features for the degradation of complex polysaccharides, particularly sulfated and fucose-rich compounds, suggesting their role in utilizing organic matter during the collapse of the bloom. Furthermore, we describe two novel genera each with a novel species (Seribacter gen. Nov., Chordibacter gen. Nov.) in accordance with the SeqCode initiative based on high quality metagenome-assembled genomes. We also propose a new name for the family MB11C04, Seribacteraceae. Our findings shed light on the ecological significance and metabolic potential of Verrucomicrobiota populations in spring bloom events.},
}
@article {pmid39637246,
year = {2024},
author = {Mahmoud, OK and Petri, F and El Zein, S and Fida, M and Diehn, FE and Verdoorn, JT and Schuetz, AN and Murad, MH and Nassr, A and Berbari, EF},
title = {What Is the Accuracy of 16S PCR Followed by Sanger Sequencing or Next-generation Sequencing in Native Vertebral Osteomyelitis? A Systematic Review and Meta-analysis.},
journal = {Clinical orthopaedics and related research},
volume = {},
number = {},
pages = {},
doi = {10.1097/CORR.0000000000003314},
pmid = {39637246},
issn = {1528-1132},
abstract = {BACKGROUND: Identifying a microorganism in patients with native vertebral osteomyelitis presents diagnostic challenges. Microorganism identification through culture-based methods is constrained by prolonged processing times and sensitivity limitations. Despite the availability of molecular diagnostic techniques for identifying microorganisms in native vertebral osteomyelitis, there is considerable variability in reported sensitivity and specificity across studies, leading to uncertainty in their clinical utility.<br><br>QUESTIONS/PURPOSES: What are the sensitivity, specificity, and diagnostic odds ratios for 16S broad-range PCR followed by Sanger sequencing (16S) and metagenomic next-generation sequencing (NGS) for detecting bacteria in native vertebral osteomyelitis?<br><br>METHODS: On June 29, 2023, we searched Cochrane, Embase, Medline, and Scopus for results from January 1970 to June 2023. Included studies involved adult patients with suspected native vertebral osteomyelitis undergoing molecular diagnostics-16S bacterial broad-range PCR followed by Sanger sequencing and shotgun or targeted metagenomic NGS-for bacteria detection. Studies involving nonnative vertebral osteomyelitis and cases of brucellar, tubercular, or fungal etiology were excluded. The reference standard for the diagnosis of native vertebral osteomyelitis was a composite clinical- and investigator-defined native vertebral osteomyelitis diagnosis. Diagnostic performance was assessed using a bivariate random-effects model. Risk of bias and diagnostic applicability were evaluated using the revised Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. After a manual screening of 3403 studies, 10 studies (5 on 16S, 5 on NGS) were included in the present analysis, from which 391 patients were included from a total of 958 patients overall. Quality assessment via QUADAS-2 criteria showed moderate risk of bias and good applicability.<br><br>RESULTS: 16S showed 78% (95% confidence interval [CI] 95% CI 31% to 96%) sensitivity and 94% (95% CI 73% to 99%) specificity, whereas NGS demonstrated 82% (95% CI 63% to 93%) sensitivity and 71% (95% CI 37% to 91%) specificity. In addition, the diagnostic ORs were 59 (95% CI 9 to 388) and 11 (95% CI 4 to 35) for 16S and NGS, respectively. Summary receiver operating characteristic curves showed high test performance for 16S (area under the curve for 16S 95% [95% CI 93% to 97%] and for NGS 89% [95% CI 86% to 92%]). Certainty in estimates was moderate because of sample size limitations.<br><br>CONCLUSION: This meta-analysis found moderate-to-high diagnostic performance of molecular methods on direct patient specimens for the diagnosis of native vertebral osteomyelitis. When used as a complementary test to microbiological analyses, a positive 16S result rules in the diagnosis of native vertebral osteomyelitis, while further studies are needed to understand the role of NGS in the diagnosis of native vertebral osteomyelitis. When available, these tests should be used in addition to conventional microbiology, especially in complex cases with extensively negative standard microbiological test results, to detect fastidious bacteria or to confirm the causative bacteria when their isolation and pathogenicity are unclear. A large sample size is needed in future research to understand the use of these techniques as standalone tests for diagnosis.<br><br>LEVEL OF EVIDENCE: Level III, diagnostic study.},
}
@article {pmid39636804,
year = {2024},
author = {Calderon, MS and Bustamante, DE and Perez, J and Fernandez-Güimac, SLJ and Mendoza, JE and Barboza, JI and Ayala, RY and Carrion, JV},
title = {Diversity and functional role of bacterial microbiota in spontaneous coffee fermentation in northern Peru using shotgun metagenomics.},
journal = {Journal of food science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1750-3841.17583},
pmid = {39636804},
issn = {1750-3841},
support = {//Consejo Nacional de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n Tecnol&#xf3;gica/ ; N&#xb0; 030-2018-FONDECYT-BM-IADT-MU//Peruvian CONCYTEC under the projects Metacaf&#xe9;/ ; N&#xb0; PE501081184-2022-PROCIENCIA//Metacaf&#xe9; 2.0/ ; //Vicerrectorado de Investigaci&#xf3;n (VRIN) de la UNTRM/ ; },
abstract = {Peru is the ninth-largest coffee producer and the largest organic coffee exporter worldwide. Specific modifications in the microbial consortia during fermentation control the flavor of coffee. It is still unclear how fermentation duration affects microbial communities. This study aimed to provide insights into the diversity and functional behavior of the bacterial microbiome during coffee fermentation in northern Peru using shotgun metagenomics. Accordingly, metagenomic DNA was extracted and sequenced from samples of the liquid fraction during the short fermentation process (SFP) in Amazonas (6 and 12 h) and long fermentation process (LFP) in Cajamarca (6, 12, 18, 24, and 36 h). Our findings indicate that common (e.g., Acetobacter, Lactobacillus, Leuconostoc, and Weissella) and unique (e.g., Acidiphilium and Methylobacterium) acid-tolerant bacteria from the SFP and LFP play crucial roles and have a positive impact on the sensory qualities of coffee. Specifically, the LFP from San Ignacio might be associated with the high sensory quality of coffee based on the release of catalytic, hydrolase, oxidoreductase, transferase, and transporter enzymes in the InterPro and KEGG profiles. Additionally, these bacterial microorganisms metabolize several compounds (e.g., isoleucine, betaine, galactose, tryptophan, arginine, and cobalamin) into volatile compounds, mainly in the LFP, enhancing the flavor and aroma of coffees. This characteristic suggests that the LFP has a stronger effect on coffee quality than does the SFP on the basis of bacterial diversity and functional prediction. These findings provide new perspectives on the potential biotechnological uses of autochthonous microorganisms to produce superior-quality coffee beans from northern Peru.},
}
@article {pmid39635985,
year = {2024},
author = {Mulders, MCF and van Koetsveld, PM and Feelders, RA and Hofland, LJ and de Herder, WW and Kraaij, R and Hofland, J},
title = {Gut microbial and functional alterations lead to metagenomic signatures for midgut neuroendocrine tumor patients and for carcinoid syndrome.},
journal = {Endocrine-related cancer},
volume = {},
number = {},
pages = {},
doi = {10.1530/ERC-24-0145},
pmid = {39635985},
issn = {1479-6821},
abstract = {Midgut neuroendocrine tumors (NET) derive from enterochromaffin cells, which have an close interrelationship with intestinal microbiota. Recently, we utilized 16S rRNA sequencing to uncover that midgut NET patients have a depleted gut microbiome and a specific fecal microbial signature. This study aims to validate these findings and to further characterize the role of microbes and microbial metabolic pathways in midgut NET patients with and without carcinoid syndrome (CS). Fecal samples from 60 midgut NET patients and 20 household-matched controls were subjected to whole metagenomics sequencing. We found that the gut microbial community composition of midgut NET patients differed from that of controls, with 2 genera, 17 species and 9 microbial pathways showing differential abundance (p < 0.001). No differences in microbial composition were observed between midgut NET patients with and without CS (p < 0.05). However, we did observe changes in inter-genus correlations of Bacteroides, Odoribacter, Parasutterella, Klebsielle, Ruminococcus and Proteobacteria when comparing these two patient groups. A signature of 16 microbial species (area under the receiver operating characteristic curve (AUROC) 0.892) or 18 microbial pathways (AUROC 0.909) accurately predicted the presence of a midgut NET. Furthermore, a microbial signature consisting of 14 functional microbial pathways distinguished CS patients from non-CS patients (AUROC 0.807). This study confirms that the gut microbiome of midgut NET patients is altered at the metagenomic level, which is not related to the presence of CS. A fecal microbial signature could constitute a novel biomarker for the diagnosis of midgut NET or CS.},
}
@article {pmid39635041,
year = {2024},
author = {Dora, D and Revisnyei, P and Mihucz, A and Kiraly, P and Szklenarik, G and Dulka, E and Galffy, G and Lohinai, Z},
title = {Metabolic pathways from the gut metatranscriptome are associated with COPD and respiratory function in lung cancer patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1381170},
pmid = {39635041},
issn = {2235-2988},
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/metabolism/physiopathology ; *Gastrointestinal Microbiome/genetics ; *Metabolic Networks and Pathways/genetics ; *Lung Neoplasms/microbiology/genetics ; Male ; *Feces/microbiology ; Female ; Aged ; Middle Aged ; Carcinoma, Non-Small-Cell Lung/genetics/microbiology ; Transcriptome ; Metagenomics/methods ; Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Streptococcus/genetics/isolation &amp; purification/metabolism ; },
abstract = {INTRODUCTION: Changes in the human gut microbiome have been linked to various chronic diseases, including chronic obstructive pulmonary disease (COPD). While substantial knowledge is available on the genomic features of fecal communities, little is known about the microbiome's transcriptional activity. Here, we analyzed the metatranscriptomic (MTR) abundance of MetaCyc pathways, SuperPathways, and protein domain families (PFAM) represented by the gut microbiome in a cohort of non-small cell lung cancer (NSCLC) patients with- or without COPD comorbidity.<br><br>METHODS: Fecal samples of 40 NSCLC patients with- or without COPD comorbidity were collected at the time of diagnosis. Data was preprocessed using the Metaphlan3/Humann3 pipeline and BioCyc[&#xa9;] to identify metabolic SuperPathways. LEfSe analysis was conducted on Pathway- and PFAM abundance data to determine COPD- and non-COPD-related clusters.<br><br>RESULTS: Key genera Streptococcus, Escherichia, Gemella, and Lactobacillus were significantly more active transcriptionally compared to their metagenomic presence. LEfSe analysis identified 11 MetaCyc pathways that were significantly overrepresented in patients with- and without COPD comorbidity. According to Spearman's rank correlation, Smoking PY showed a significant negative correlation with Glycolysis IV, Purine Ribonucleoside Degradation and Glycogen Biosynthesis I, and a significant positive correlation with Superpathway of Ac-CoA Biosynthesis and Glyoxylate cycle, whereas forced expiratory volume in the first second (FEV1) showed a significant negative correlation with Glycolysis IV and a significant positive correlation with Glycogen Biosynthesis I. Furthermore, COPD patients showed a significantly increased MTR abundance in ~60% of SuperPathways, indicating a universally increased MTR activity in this condition. FEV1 showed a significant correlation with SuperPathways Carbohydrate degradation, Glycan biosynthesis, and Glycolysis. Taxonomic analysis suggested a more prominent MTR activity from multiple Streptococcus species, Enterococcus (E.) faecalis, E. faecium and Escherichia (E.) coli than expected from their metagenomic abundance. Multiple protein domain families (PFAMs) were identified as more associated with COPD, E. faecium, E.coli, and Streptococcus salivarius, contributing the most to these PFAMs.<br><br>CONCLUSION: Metatranscriptome analysis identified COPD-related subsets of lung cancer with potential therapeutic relevance.},
}
@article {pmid39634420,
year = {2024},
author = {Lu, R and Li, D and Guo, Y and Cui, Z and Wei, Z and Fan, G and Zhang, W and Wang, Y and Gu, Y and Han, M and Liu, S and Meng, L},
title = {Comparative metagenomics highlights the habitat-related diversity in taxonomic composition and metabolic potential of deep-sea sediment microbiota.},
journal = {Heliyon},
volume = {10},
number = {22},
pages = {e39055},
pmid = {39634420},
issn = {2405-8440},
abstract = {Sediment plays a pivotal role in deep-sea ecosystems by providing habitats for a diverse range of microorganisms and facilitates the cycling processes of carbon, sulfur and nitrogen. Beyond the normal seafloor (NS), distinctive geographical features such as cold seeps (CS) and hydrothermal vent (HV) are recognized as life oases harboring highly diverse microbial communities. A global atlas of microorganisms can reveal the notable association between geological processes and microbial colonization. However, a comprehensive understanding of the systematic comparison of microbial communities in sediments across various deep-sea regions worldwide and their contributions to Earth's elemental cycles remains limited. Analyzing metagenomic data from 163 deep-sea sediment samples across 73 locations worldwide revealed that microbial communities in CS sediments exhibited the highest richness and diversity, followed by HV sediments, with NS sediments showing the lowest diversity. The NS sediments were predominantly inhabited by Nitrosopumilaceae, a type of ammonia-oxidizing archaea (AOA). In contrast, CSs and HVs were dominated by ANME-1, a family of anaerobic methane-oxidizing archaea (ANME), and Desulfofervidaceae, a family of sulfate-reducing bacteria (SRB), respectively. Microbial networks were established for each ecosystem to analyze the relationships and interactions among different microorganisms. Additionally, we analyzed the metabolic patterns of microbial communities in different deep-sea sediments. Despite variations in carbon fixation pathways in ecosystems with different oxygen concentrations, carbon metabolism remains the predominant biogeochemical cycle in deep-sea sediments. Benthic ecosystems exhibit distinct microbial potentials for sulfate reduction, both assimilatory and dissimilatory sulfate reduction (ASR and DSR), in response to different environmental conditions. The presence of nitrogen-fixing microorganisms in CS sediments may influence the global nitrogen balance. In this study, the significant differences in the taxonomic composition and functional potential of microbial communities inhabiting various deep-sea environments were investigated. Our findings emphasize the importance of conducting comparative studies on ecosystems to reveal the complex interrelationships between marine sediments and global biogeochemical cycles.},
}
@article {pmid39634324,
year = {2024},
author = {Shao, L and Zhang, B and Song, Y and Lyu, Z and Zhang, W and Yang, W and Fu, J and Li, J and Shi, J},
title = {Mucosal Hub Bacteria as Potential Targets for Improving High-Fat Diet-Related Intestinal Barrier Injury.},
journal = {The Canadian journal of infectious diseases &amp; medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale},
volume = {2024},
number = {},
pages = {3652740},
pmid = {39634324},
issn = {1712-9532},
abstract = {Background: Intestinal barrier injury contributes to multiple diseases such as obesity and diabetes, whereas no treatment options are available. Methods: Due to close interactions between mucosal microbiome and intestinal barrier, we evaluated the potential of mucosal bacteria in providing targets for high-fat diet (HFD)-related intestinal barrier injury. Whole-genome metagenomics was used to evaluate mucosal microbiome, while intestinal barrier injury was estimated using serum LPS, FITC-dextran intensity, and ZO-1 protein. Results: We found that HFD induced significant fat accumulation in epididymal tissue at weeks 4 and 12, while ALT, LDL, and TC increased at week 12. Intestinal barrier injury was confirmed by elevated serum LPS at both weeks, upregulated FITC-dextran intensity, and decreased ZO-1 protein at week 12. Fourteen species such as Phocaeicola vulgatus differed in HFD-fed mice. The co-occurrence network of mucosal microbiome shifted from scale-free graph in controls to nearly random graph in HFD-fed mice. Besides, 10 hub bacteria especially Bacteroides ovatus decreased drastically in both mucosal and fecal samples of HFD-fed mice, correlated with intestinal permeability, ALT, and KEGG pathways such as "Mitochondrial biogenesis" and "metabolism". Moreover, Bacteroides ovatus has been confirmed to improve intestinal barrier function in a recent study. Conclusion: Mucosal hub bacteria can provide potential targets for improving HFD-related intestinal barrier function.},
}
@article {pmid39633808,
year = {2024},
author = {Guo, Y and Feng, H and Du, L and Yu, Z},
title = {Patterns of antibiotic resistance genes and virulence factor genes in the gut microbiome of patients with osteoarthritis and rheumatoid arthritis.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1427313},
pmid = {39633808},
issn = {1664-302X},
abstract = {BACKGROUND: The gut microbiome compositions of osteoarthritis (OA) and rheumatoid arthritis (RA) patients have been revealed; however, the functional genomics, particularly antibiotic resistance genes (ARGs) and virulence factor genes (VFGs), have not yet been explored.<br><br>METHODS: We used gut metagenomic data to elucidate the distribution of ARGs and VFGs. Building on these differences in gut microbiome, we developed a diagnostic model using a random forest classifier based on ARG and VFG abundances.<br><br>RESULTS: Our results indicated that both OA and RA patients exhibit significantly higher alpha diversity in ARGs, as measured by observed genes, the Shannon index, and the Simpson index, compared to healthy controls. However, this increased diversity is not significantly different between OA and RA patients. In contrast, VFGs showed higher diversity in RA patients than in healthy individuals, which was not as pronounced in OA patients. An analysis of the top 20 ARGs and VFGs revealed a largely similar composition between the three groups, with notable exceptions of certain genes that were uniquely enriched in either OA or RA patients. This suggests unique microbial patterns associated with each condition. Our beta diversity analysis further demonstrated distinct distributions of ARG and VFG profiles across the three groups, with several genes significantly enriched in both OA and RA patients, indicating potential markers for these diseases. The model achieved high accuracy (74.7-83.6%) when distinguishing both OA and RA from healthy controls using ARG profiles and substantial accuracy using VFG profiles.<br><br>CONCLUSION: These results support the potential of ARGs and VFGs as reliable biomarkers for diagnosing OA and RA.},
}
@article {pmid39633804,
year = {2024},
author = {Sharma, N and Das, BK and Bhattacharjya, BK and Chaudhari, A and Behera, BK and Kumar, AP and Chakraborty, HJ},
title = {Metagenomic insights into microbial community, functional annotation, and antibiotic resistance genes in Himalayan Brahmaputra River sediment, India.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1426463},
pmid = {39633804},
issn = {1664-302X},
abstract = {INTRODUCTION: The Brahmaputra, a major transboundary river of the Himalayas flowing predominantly through Northeast India, particularly Assam, is increasingly endangered by contamination due to rapid urbanization and anthropogenic pressures. These environmental changes pose significant risks at the microbial level, affecting nutrient cycling and productivity, and thereby impacting river ecosystem health. The next-generation sequencing technology using a metagenomics approach has revolutionized our understanding of the microbiome and its critical role in various aquatic environments.<br><br>METHODS: The present study aimed to investigate the structure of the bacterial community and its functional potentials within the sediments of the Brahmaputra River, India, using high-throughput shotgun metagenomics. Additionally, this study sought to explore the presence of antimicrobial resistance genes in the river's sediment.<br><br>RESULTS AND DISCUSSION: Shotgun metagenomics revealed a diverse bacterial community comprising 31 phyla, 52 classes, 291 families, 1,016 genera, and 3,630 species. Dominant phyla included Pseudomonadota (62.47-83.48%), Actinobacteria (11.10-24.89%), Bacteroidetes (0.97-3.82%), Firmicutes (0.54-3.94%), Cyanobacteria (0.14-1.70%), and Planctomycetes (0.30-0.78%). Functional profiling highlighted significant involvement in energy metabolism, amino acid and central carbon metabolism, stress response, and degradation pathways, emphasizing the microbial community's role in ecosystem functioning and resilience. Notably, 50 types of antibiotic resistance genes (ARGs) were detected, with resistance profiles spanning multidrug, aminoglycoside, &#x3b2;-lactam, fluoroquinolone, rifampicin, sulfonamide, and tetracycline classes. Network analysis underscored the intricate relationships among ARG subtypes, suggesting potential mechanisms of resistance propagation. Furthermore, plasmid-related genes and 185 virulence factor genes (VFGs) were identified, indicating additional layers of microbial adaptation and potential pathogenicity within the river sediments. This comprehensive microbial and functional profiling of the Brahmaputra's sediment metagenome provides crucial insights into microbial diversity, resistance potential, and ecological functions, offering a foundation for informed management and mitigation strategies to preserve river health and mitigate pollution impacts.},
}
@article {pmid39633723,
year = {2024},
author = {Heinzinger, M and Weissenow, K and Sanchez, JG and Henkel, A and Mirdita, M and Steinegger, M and Rost, B},
title = {Bilingual language model for protein sequence and structure.},
journal = {NAR genomics and bioinformatics},
volume = {6},
number = {4},
pages = {lqae150},
pmid = {39633723},
issn = {2631-9268},
abstract = {Adapting language models to protein sequences spawned the development of powerful protein language models (pLMs). Concurrently, AlphaFold2 broke through in protein structure prediction. Now we can systematically and comprehensively explore the dual nature of proteins that act and exist as three-dimensional (3D) machines and evolve as linear strings of one-dimensional (1D) sequences. Here, we leverage pLMs to simultaneously model both modalities in a single model. We encode protein structures as token sequences using the 3Di-alphabet introduced by the 3D-alignment method Foldseek. For training, we built a non-redundant dataset from AlphaFoldDB and fine-tuned an existing pLM (ProtT5) to translate between 3Di and amino acid sequences. As a proof-of-concept for our novel approach, dubbed Protein 'structure-sequence' T5 (ProstT5), we showed improved performance for subsequent, structure-related prediction tasks, leading to three orders of magnitude speedup for deriving 3Di. This will be crucial for future applications trying to search metagenomic sequence databases at the sensitivity of structure comparisons. Our work showcased the potential of pLMs to tap into the information-rich protein structure revolution fueled by AlphaFold2. ProstT5 paves the way to develop new tools integrating the vast resource of 3D predictions and opens new research avenues in the post-AlphaFold2 era.},
}
@article {pmid39632779,
year = {2024},
author = {Eyal, N and Williams, B and Esvelt, KM and Bambauer, J},
title = {Metagenomic Sequencing for Early Detection of Future Engineered Pandemics: Foreshadowing the Privacy Challenge.},
journal = {Health security},
volume = {},
number = {},
pages = {},
doi = {10.1089/hs.2023.0140},
pmid = {39632779},
issn = {2326-5108},
}
@article {pmid39632378,
year = {2024},
author = {Li, Y and Hu, W and Lin, B and Ma, T and Zhang, Z and Hu, W and Zhou, R and Kwok, LY and Sun, Z and Zhu, C and Zhang, H},
title = {Omic characterizing and targeting gut dysbiosis in children with autism spectrum disorder: symptom alleviation through combined probiotic and medium-carbohydrate diet intervention - a pilot study.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2434675},
doi = {10.1080/19490976.2024.2434675},
pmid = {39632378},
issn = {1949-0984},
mesh = {Humans ; *Autism Spectrum Disorder/diet therapy/microbiology ; Pilot Projects ; *Probiotics/administration &amp; dosage ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/diet therapy/therapy ; Male ; Child ; Female ; *Feces/microbiology/chemistry ; Child, Preschool ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; Dietary Carbohydrates/metabolism/administration &amp; dosage ; Bifidobacterium animalis ; },
abstract = {Autism spectrum disorder (ASD) currently lacks effective diagnostic and therapeutic approaches. Disruptions in the gut ecosystem have been observed in individuals with ASD, suggesting that targeting gut microbiota through probiotic and dietary supplementation may serve as a potential treatment strategy. This two-phase study aimed to characterize the fecal metagenome of children with ASD and investigate the beneficial effects of a combined probiotic and medium-carbohydrate intervention in ASD. Fecal metagenomes of children with ASD were compared to those of typically developing children, revealing intestinal dysbiosis in ASD, characterized by reduced levels of Prevotella sp. Dialister invisus, and Bacteroides sp. along with increased predicted abundances of inosine, glutamate, xanthine, and methylxanthine. The gut bacteriome and phageome exhibited high cooperativity. In a 3-month pilot study, Bifidobacterium animalis subsp. lactis Probio-M8 (Probio-M8) was administered alongside a medium-carbohydrate diet to Chinese children with ASD. The primary endpoint was the Childhood Autism Rating Scale (CARS), while the secondary endpoint was the Gastrointestinal Symptom Rating Scale (GSRS). A total of 72 autistic children were initially recruited for the intervention study, but only 53 completed the intervention. Probio-M8, in combination with dietary intervention, significantly improved CARS and GSRS scores, increased fecal levels of Bifidobacterium animalis, Akkermansia muciniphila, Fusicatenibacter saccharivorans, and Sutterella sp. while also reducing Blautia obeum (Benjamini-Hochberg corrected p ≤ 0.05 for all cases). The intervention also modulated fecal metabolites associated with the metabolism of amino acids (lysine), neurotransmitters (glutamate, γ-aminobutyric acid), polyunsaturated fatty acids (arachidonate, myristic acid), and vitamin B3. In conclusion, Probio-M8 combined with medium-carbohydrate diet effectively improved ASD symptoms, with associated changes in the gut microbiome and metabolome, supporting its potential as an adjunctive therapy for ASD.},
}
@article {pmid39632177,
year = {2024},
author = {Li, D and Li, L and Wang, P and Zhang, W},
title = {The application value of metagenomic next-generation sequencing technology in the detection of pathogens in patients with pneumonia after initial treatment failure.},
journal = {Asian journal of surgery},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.asjsur.2024.11.113},
pmid = {39632177},
issn = {0219-3108},
}
@article {pmid39631543,
year = {2024},
author = {Qu, M and Zheng, Y and Cheng, Z and Shi, Y and Wang, W and Wu, X and Chen, J},
title = {Mechanism of chlorobenzene removal in biotrickling filter enhanced by non-thermal plasma: Insights from biodiversity and functional gene perspectives.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131931},
doi = {10.1016/j.biortech.2024.131931},
pmid = {39631543},
issn = {1873-2976},
abstract = {Biotrickling filter (BTF) technology is inefficient in the treatment of Cl-containing volatile organic compounds (VOCs) such as chlorobenzene (CB). This study adopted non-thermal plasma (NTP) as a pretreatment and conducted in-depth analyses, especially in microorganisms, to investigate strengthening mechanism of a NTP to a BTF in the process. The introduction of NTP enhance efficiency of CB removal from 65 % to 90 %, and CO2 generation from 60 % to 85 %. It is found that the protein content of the extracellular polymeric substances increases from 212 × 10[-3] mg·g[-1] filler to 299 × 10[-3] mg·g[-1] filler, thus CB capturing and utilization enhanced. Metagenomic analysis showed that bacteria with CB-degrading properties were enriched in BTF, and CB was involved in cellular metabolism as a carbon source. The presence of active substances from NTP is found to stimulate the ability of BTF treatment. The findings of this study will provide theoretical support for the application of NTP-BTF technology.},
}
@article {pmid39631542,
year = {2024},
author = {Xiong, Z and Chen, X and Zou, Z and Peng, L and Zou, L and Liu, B and Li, Q},
title = {Improving efficiency of bacterial degradation of polyethylene microplastics using atmospheric and room temperature plasma mutagenesis.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131930},
doi = {10.1016/j.biortech.2024.131930},
pmid = {39631542},
issn = {1873-2976},
abstract = {In this study, the bacterium XZ-A was genetically modified using atmospheric and room temperature plasma mutagenesis (ARTP) to increase the degradation efficiency of polyethylene microplastics (PE-MPs) by up to 53.65 %. After 50 d of biodegradation, the mutagenized bacterium XZ-60S caused significant changes in the morphology, structure, thermal stability, and molecular weight of PE-MPs. The number average molecular weights and weight average molecular weights of the PE-MPs were significantly reduced by approximately 15.21 % and 4.80 %, respectively. Comparative genomic and transcriptomic analyses showed that XZ-60S had a total of 106 single nucleotide polymorphic sites, and the expression of genes encoding laccases was significantly increased; this may explain the improved degradation of PE-MPs by XZ-60S. In this study, the degradation of PE-MPs by bacteria was improved through ARTP mutagenesis, which provides a reference for selecting and breeding bacteria that are highly efficient at degrading PE-MPs.},
}
@article {pmid39630952,
year = {2024},
author = {Gao, F and Shen, Y and Wu, H and Laue, HE and Lau, FK and Gillet, V and Lai, Y and Shrubsole, MJ and Prada, D and Zhang, W and Liu, Z and Bellenger, JP and Takser, L and Baccarelli, AA},
title = {Associations of Stool Metal Exposures with Childhood Gut Microbiome Multiomics Profiles in a Prospective Birth Cohort Study.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c09642},
pmid = {39630952},
issn = {1520-5851},
abstract = {Metal exposures are closely related to childhood developmental health. However, their effects on the childhood gut microbiome, which also impacts health, are largely unexplored using microbiome multiomics including the metagenome and metatranscriptome. This study examined the associations of fecal profiles of metal/element exposures with gut microbiome species and active functional pathways in 8- to 12-year-old children (N = 116) participating in the GESTation and Environment (GESTE) cohort study. We analyzed 19 stool metal and element concentrations (B, Na, Mg, Al, K, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Mo, Cd, Ba, and Pb). Covariate-adjusted linear regression models identified several significant microbiome associations with continuous stool metal/element concentrations. For instance, Zn was positively associated with Turicibacter sanguinis (coef = 1.354, q-value = 0.039) and negatively associated with Eubacterium eligens (coef = -0.794, q-value = 0.044). Higher concentrations of Cd were associated with lower Eubacterium eligens (coef = -0.774, q-value = 0.045). Additionally, a total of 490 significant functional pathways such as biosynthesis and degradation/utilization/assimilation were identified, corresponding to different functions, including amino acid synthesis and carbohydrate degradation. Our results suggest links among metal exposures, pediatric gut microbiome multiomics, and potential health implications. Future work will further explore their relation to childhood health.},
}
@article {pmid39630239,
year = {2024},
author = {Boonyapakron, K and Keiser, B and Prabmark, K and Aiewviriyasakul, K and Arunrattanamook, N and Jaruwat, A and Chitnumsub, P and Li, JY and Wong, TS and Zhao, XQ and Liu, CG and Wei, DQ and Champreda, V},
title = {Hyperthermophilic xylanase and thermophilicity analysis by molecular dynamic simulation with quantum mechanics.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {526},
pmid = {39630239},
issn = {1432-0614},
support = {B16F640052//PMU-B/ ; Grant No. 32070662//National Science Foundation of China/ ; 61832019//National Science Foundation of China/ ; 32030063//National Science Foundation of China/ ; 2023YFE0199200//Key Technologies Research and Development Program of Anhui Province/ ; LTSRF1819\15\21//Royal Academy of Engineering/ ; },
mesh = {*Molecular Dynamics Simulation ; *Endo-1,4-beta Xylanases/chemistry/genetics/metabolism ; *Enzyme Stability ; *Xylans/metabolism/chemistry ; *Oligosaccharides/metabolism/chemistry ; *Glucuronates/metabolism/chemistry ; Substrate Specificity ; Hot Temperature ; Cellulose/metabolism ; Hydrogen Bonding ; Quantum Theory ; Disaccharides/metabolism/chemistry ; Metagenome ; },
abstract = {Thermophilic xylanases catalyzing the cleavage of β-1,4-glycosidic bonds in xylan have applications in food, feed, biorefinery, and pulp industries. In this study, a hyperthermophilic endo-xylanase was obtained by further enhancement of thermal tolerance of a thermophilic GH11 xylanase originated from metagenome of bagasse pile based on rational design. Introducing N13F and Q34L to the previously reported X11P enzyme shifted the optimal working temperature to 85 °C and led to 20.7-fold improvement in thermostability at 90 °C along with a marked increase in Tm to 93.3 °C. X11PNQ enzyme converted xylan to prebiotic xylooligosaccharides with high specificity on xylobiose to xylohexaose and high operational stability at 85 °C, resulting in 10.3-folds yield improvement compared to the parental enzyme. Molecular dynamic simulation and quantum mechanical analysis revealed improved H-bonding networks within GH11 xylanase principal domains and greater dynamic cross-correlations. A novel thermostabilization mechanism by π-amide interaction with slightly lower interaction energy than the native H-bond, but compensated by increased occurrence frequency was firstly demonstrated for thermophilic enzymes. The enzyme represents one of the most thermostable xylanases ever reported with biotechnological potential. KEY POINTS: • Hyperthemophilic xylanase X11PNQ was obtained by rational design engineering. • X11PNQ showed specificity to prebiotic xylooligosaccharides (XOS) at 85 °C with improved t1/2 at 90 °C. • Novel thermostabilization by π-amide interaction was demonstrated by MD/QM.},
}
@article {pmid39629792,
year = {2024},
author = {González-García, S and Hamdan-Partida, A and Pérez-Ramos, J and Aguirre-Garrido, JF and Bustos-Hamdan, A and Bustos-Martínez, J},
title = {Comparison of the bacterial microbiome in the pharynx and nasal cavity of persistent, intermittent carriers and non-carriers of Staphylococcus aureus.},
journal = {Journal of medical microbiology},
volume = {73},
number = {12},
pages = {},
pmid = {39629792},
issn = {1473-5644},
mesh = {Humans ; *Pharynx/microbiology ; *Staphylococcus aureus/isolation &amp; purification/genetics ; *Carrier State/microbiology ; *Nasal Cavity/microbiology ; *Microbiota ; *Staphylococcal Infections/microbiology ; Male ; Female ; Adult ; Young Adult ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; },
abstract = {Introduction. Staphylococcus aureus is a bacterium that colonizes various human sites. The pharynx has been considered as a site of little clinical relevance and little studied. Recently, it has been reported that S. aureus can colonize more the pharynx than the nose. In addition, S. aureus can persist in these sites for prolonged periods of time.Hypothesis. The composition of the pharyngeal and nasal microbiome will differ between persistent, intermittent carriers and non-carriers of S. aureus.Aim. Determine whether the pharyngeal and nasal microbiome is different between carriers and non-carriers of S. aureus.Methodology. S. aureus carriers were monitored by means of pharyngeal and nasal exudates of apparently healthy adult university students for 3 months. Samples from individuals of the same carrier type were pooled, and DNA was extracted and the 16S rRNA was sequenced. The sequences were analysed in MOTHUR v.1.48.0 software, by analysing the percentages of relative abundance in the STAMP 2.1.3 program, in addition to the predictive analysis of metabolic pathways in PICRUSt2.Results. A greater colonization of S. aureus was found in the pharynx than in the nose. The microbiomes of S. aureus carriers and non-carriers do not show significant differences. The main microbiome difference found was between pharyngeal and nasal microbiomes. No significant differences were found in the abundance of the genus Staphylococcus in pharyngeal and nasal S. aureus carriers and non-carriers. The nasal microbiome was found to have more variation compared to the pharyngeal microbiome, which appears to be more stable between individuals and pools. Predictive analysis of metabolic pathways showed a greater presence of Staphylococcus-associated pathways in the nose than in the pharynx.Conclusion. S. aureus can colonize and persist in the pharynx in equal or greater proportion than in the nose. No statistically significant differences were found in the microbiome of the pharyngeal and nasal carriers and non-carriers of S. aureus, but the pharyngeal and nasal microbiomes are different independent of the type of S. aureus carrier or non-carrier. Therefore, the microbiome apparently does not influence the persistence of S. aureus.},
}
@article {pmid39629232,
year = {2024},
author = {Zhang, W and Xiao, L and Shan, X and Dai, B and Tang, C and Xian, J and Yu, Y},
title = {Case report: Detection of non-O1/non-O139 Vibrio cholerae in a patient with hepatic space-occupying lesions using metagenomic next-generation sequencing.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1483027},
pmid = {39629232},
issn = {2296-858X},
abstract = {INTRODUCTION/BACKGROUND: Vibrio cholerae is the causative agent of the human intestinal infectious disease cholera, which includes a variety of serogroups. However, there have been very few cases of hepatic space-occupying lesions associated with this infection. Currently, there are various methods for detecting this pathogen, including metagenomic sequencing, which enables quicker and more accurate identification. In this study, metagenomic sequencing is employed to accurately identify non-O1/O139 Vibrio cholerae infections by analyzing the genetic material present in clinical samples.<br><br>PRESENTATION OF CASE: A 75-year-old man presented with diarrhea and fever after consuming crabs. The initial treatment improved the diarrhea, but a liver abscess developed later. Magnetic resonance imaging (MRI) of the liver revealed a hepatic space-occupying lesion. Upon further investigation, a Gram-negative, rod-shaped bacterium was cultured from the patient's liver puncture fluid, and Vibrio cholerae was detected in the same fluid using metagenomic next-generation sequencing (mNGS). The pathogen was confirmed to be non-O1/non-O139 Vibrio cholerae (NOVC) using polymerase chain reaction (PCR). Following treatment with piperacillin/tazobactam sodium and moxifloxacin, the patient's body temperature returned to normal, the liver abscess improved significantly, and he was subsequently discharged from the hospital.<br><br>DISCUSSION: This case study describes an elderly male patient with a hepatic space-occupying lesion. Multiple cultures of specimens failed to identify the underlying cause; however, advanced techniques such as mNGS and PCR confirmed an NOVC infection. This indicates that mNGS can serve as a valuable tool in diagnosing cases of unexplained liver infections.<br><br>CONCLUSION: The use of mNGS is significant for detecting and clinically diagnosing infectious pathogens in patients with unexplained space-occupying lesions.},
}
@article {pmid39629213,
year = {2024},
author = {Ramos, S and Júnior, E and Alegria, O and Vieira, E and Patroca, S and Cecília, A and Moreira, F and Nunes, A},
title = {Metagenomics insights into bacterial diversity and antibiotic resistome of the sewage in the city of Belém, Pará, Brazil.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1466353},
pmid = {39629213},
issn = {1664-302X},
abstract = {INTRODUCTION: The advancement of antimicrobial resistance is a significant public health issue today. With the spread of resistant bacterial strains in water resources, especially in urban sewage, metagenomic studies enable the investigation of the microbial composition and resistance genes present in these locations. This study characterized the bacterial community and antibiotic resistance genes in a sewage system that receives effluents from various sources through metagenomics.<br><br>METHODS: One liter of surface water was collected at four points of a sewage channel, and after filtration, the total DNA was extracted and then sequenced on an NGS platform (Illumina&#xae; NextSeq). The sequenced data were trimmed, and the microbiome was predicted using the Kraken software, while the resistome was analyzed on the CARD webserver. All ecological and statistical analyses were performed using the. RStudio tool.<br><br>RESULTS AND DISCUSSION: The complete metagenome results showed a community with high diversity at the beginning and more restricted diversity at the end of the sampling, with a predominance of the phyla Bacteroidetes, Actinobacteria, Firmicutes, and Proteobacteria. Most species were considered pathogenic, with an emphasis on those belonging to the Enterobacteriaceae family. It was possible to identify bacterial groups of different threat levels to human health according to a report by the U.S. Centers for Disease Control and Prevention. The resistome analysis predominantly revealed genes that confer resistance to multiple drugs, followed by aminoglycosides and macrolides, with efflux pumps and drug inactivation being the most prevalent resistance mechanisms. This work was pioneering in characterizing resistance in a sanitary environment in the Amazon region and reinforces that sanitation measures for urban sewage are necessary to prevent the advancement of antibiotic resistance and the contamination of water resources, as evidenced by the process of eutrophication.},
}
@article {pmid39629129,
year = {2024},
author = {Zhao, Q and Lu, Y and Duan, J and Du, D and Pu, Q and Li, F},
title = {Gut microbiota depletion and FXR inhibition exacerbates zonal hepatotoxicity of sunitinib.},
journal = {Theranostics},
volume = {14},
number = {18},
pages = {7219-7240},
pmid = {39629129},
issn = {1838-7640},
mesh = {Animals ; *Sunitinib/toxicity ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Chemical and Drug Induced Liver Injury/pathology/etiology ; *Liver/drug effects/pathology ; *Mice, Knockout ; *Receptors, Cytoplasmic and Nuclear/metabolism ; Male ; Hepatocytes/drug effects ; Mice, Inbred C57BL ; Endothelial Cells/drug effects ; Apoptosis/drug effects ; Bacteroidetes/drug effects ; Autophagy/drug effects ; },
abstract = {Rationale: Sunitinib is a small-molecule tyrosine kinase inhibitor associated with the side-effect of liver injury. The impaired cell type in liver and the hepatotoxicity mechanisms is still unclear. Methods: Spatial metabolomics, transmission electron microscopy, immunofluorescence co-staining, and isolation of bile duct cells and liver sinusoidal endothelial cells (LSECs) were used to evaluate the zonated hepatotoxicity of sunitinib. Farnesoid X receptor (FXR) conditional knockout mice, metagenomics analysis, bacteria clearance, bacterial culture, Parabacteroides distasonis and 3-oxolithocholic acid supplementation were used to evaluate the hepatotoxicity mechanisms of sunitinib. Results: Phenotype analysis found that hepatic autophagy, apoptosis, and mitochondrial injury were observed in vivo or in vitro after sunitinib treatment. By using spatial metabolomics and isolation of bile duct cells and LSECs, the zonated drug toxicity was observed around the portal vein. Hepatocytes, bile duct cells, and LSECs were damaged after sunitinib treatment. FXR inhibition and gut microbiota depletion aggravated sunitinib-induced liver injury. For diurnal variation, sunitinib-induced liver injury was enhanced at night compared with that at day, and FXR and gut microbiota participated in circadian rhythmic hepatotoxicity induced by sunitinib. Conclusions: Our data suggested activation of FXR and Parabacteroides distasonis supplementation may be used to improve sunitinib-induced hepatotoxicity.},
}
@article {pmid39628602,
year = {2024},
author = {Xu, M and Guo, Y and Song, X and Li, L and Xu, Z and Zhao, J and Zhao, J and Lin, H and Dong, S and Lu, J and Ding, W and Liu, P and Tang, J},
title = {Analysis on microbial communities and characteristic flavor metabolic of PXDB-meju by partially substituting wheat flour with soybean flour and gluten flour.},
journal = {Current research in food science},
volume = {9},
number = {},
pages = {100904},
pmid = {39628602},
issn = {2665-9271},
abstract = {Pixian Douban (PXDB) is one of the most popular condiments in China due to its unique flavor. Wheat flour that contains abundant nutrients is an important raw material in producing flavors during PXDB fermentation. In this study, wheat flour was substituted with soybean flour and gluten flour that have higher proteins in portions of 10.4% and 4.2% (F1), 8.9% and 7.2% (F2), 9.6% and 5.8% (F3). The results indicated that the substitutions increased the amino acid nitrogen content and improved flavor quality compared with traditional group (CT). Especially, the key amino acids including spartate, glutamic, arginine and lysine, and the phenylacetaldehyde as one of the most important volatile compounds exhibited preferable higher contents in F2 group than those in CT group. Metagenomic analysis showed that the abundances of predominant bacteria, including Kosakonia_cowanii, unclassified_f__Enterobacteriaceae and unclassified_g__Enterobacter, were higher in the F2 compared to the CT. Lupinus_albus and Plutella_xylostella were the top two fungi in relative abundance, with higher growth rates in F2 than in CT. Furthermore, metabolism pathway analysis revealed higher relative abundance of enzymes producing key amino acids and phenethylaldehyde in the F2 compared to the CT. Meanwhile, these enzymes were exclusively annotated to the Kosakonia_cowanii, Bacillus_velezensis and Escherichia_coli in F2. This study provided a theoretical foundation for improving PXDB flavor quality in industry production.},
}
@article {pmid39628590,
year = {2024},
author = {Zhang, ZF and Li, M},
title = {The way to uncovering and utilizing marine microbial resources.},
journal = {Engineering microbiology},
volume = {4},
number = {4},
pages = {100175},
pmid = {39628590},
issn = {2667-3703},
abstract = {Recently, Chen et al. published their breakthrough results on a marine microbial genomic catalog and genetic potentials in bioprospecting in Nature, providing unprecedented opportunities for development and utilization of genetic resources of marine microorganisms. To highlight this article, we summarized and highlighted their breakthroughs seriatim.},
}
@article {pmid39628383,
year = {2024},
author = {Wang, H and Feng, L and Pei, Z and Zhao, J and Lu, S and Lu, W},
title = {Gut microbiota metabolism of branched-chain amino acids and their metabolites can improve the physiological function of aging mice.},
journal = {Aging cell},
volume = {},
number = {},
pages = {e14434},
doi = {10.1111/acel.14434},
pmid = {39628383},
issn = {1474-9726},
support = {2022YFF1100403//National Key Research and Development Program of China/ ; HB2023003//Top Talent Support Program for young and middle-aged people of Wuxi Health Committee/ ; },
abstract = {The metabolism of branched-chain amino acids by gut microbiota can improve overall health and may reverse aging. In this study, we investigated Parabacteroides merdae, a gut microbe that is known to catabolise branched-chain amino acids (BCAAs). Three metabolites of BCAAs isovalerate, 2-methylbutyrate, and isobutyrate were used to treat D-gal induced aging mice. The results showed that these treatments could delay aging in mice by providing health benefits in reducing oxidative stress and inflammation, improving muscle capacity, reversing brain acetylcholine levels, and regulating blood glucose. The mechanism was preliminarily explored by combining the gut microbiota metagenome and faecal serum metabolome. Parabacteroides merdae altered the species composition and structure of the gut microbiota in mice. Increasing the abundance of beneficial bacteria, such as Bifidobacterium pseudolongum. Three metabolites affects the gut microbiota and the body's pathways of protein and improves the overall health through a variety of signaling pathways. Overall, regulating the gut microbiota involved in branched-chain amino acid metabolism to bring health benefits may be a new way of reversing aging.},
}
@article {pmid39628196,
year = {2024},
author = {Li, ZX and Li, JH and Zhang, Q and Lu, JJ and Gao, CH and Jin, DS and Xu, MG},
title = {[Response and Assembly Process of Soil Microbial Communities Under Different Reclamation Measures].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {45},
number = {12},
pages = {7326-7336},
doi = {10.13227/j.hjkx.202312247},
pmid = {39628196},
issn = {0250-3301},
mesh = {*Soil Microbiology ; *Fungi/classification ; *Bacteria/classification/genetics/growth &amp; development/isolation &amp; purification ; Mining ; Nitrogen ; Soil/chemistry ; Phosphorus ; Environmental Restoration and Remediation/methods ; Microbiota ; Ecosystem ; },
abstract = {Reclamation is essential for restoring the ecological function of soil in mining areas. However, the microbiological mechanism of soil ecological function reconstruction under different reclamation measures still needs to be clarified. Clarifying the characteristics of soil bacterial and fungal communities, assembly mechanisms, and their relationship with physicochemical properties under different reclamation measures is crucial for reshaping the ecological stability of soil in mining areas. Metagenomic sequencing technology was combined with the null model and neutral model to analyze the differences in soil microbial diversity, community composition, network structure, and community assembly process between the reclaimed natural recovery area （LH） and the reclamation fertilization area （MM）. The results suggested that： ① Compared with that in the LH treatment, the MM treatment significantly increased the soil nutrient content, and the total nitrogen （TN）, total phosphorus （TP）, available phosphorus （AP）, and available potassium （AK） contents increased by 34.70%, 72.72%, 468.98%, and 45.74%, respectively （P<0.05）. ② The dominant bacterial and fungal communities did not change under the LH and MM treatments； however, the abundance of bacterial communities changed significantly. Compared with that in the LH treatment, the relative abundance of Acidobacteria increased significantly by 5.4% in the MM treatment, while the relative abundance of Candidatus Rokubacteria decreased significantly by 235.72% （P<0.05）. Under different reclamation measures, the indicator microorganisms of bacterial and fungal communities changed. ③ Compared with that in the LH treatment, the MM treatment increased the complexity of bacterial networks, decreased the complexity of fungal networks, and increased the number of soil bacterial nodes and links. The reclamation measures transformed the key bacterial groups from Proteobacteria to Candidatus Rokubacteria and Planctomycetes. The key group of fungi was Ascomycota. 4.） The deterministic process dominated the assembly of bacterial and fungal communities. Homogeneous selection contributed the most to the bacterial community assembly in the LH treatment, and heterogeneous selection contributed the most to the MM treatment. The fungal communities were all dominated by heterogeneous selection. These results provide new insights into the soil microbial community structure and ecological function restoration in coal mining subsidence reclamation areas.},
}
@article {pmid39628107,
year = {2024},
author = {Zou, Y and Zou, X and Lin, C and Han, C and Zou, Q},
title = {Inference of functional differentiation of intestinal microbes between two wild zokor species based on metagenomics.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.8587},
pmid = {39628107},
issn = {1526-4998},
support = {//National Promoted Program of scientific and technological achievements in Forestry and Grassland/ ; //the National Key Program of Research and Development/ ; },
abstract = {BACKGROUND: Currently, there are fewer studies on the intestinal microbes of wild zokors, and it is unclear how zokors adapt to special underground environments by regulating their intestinal microbes. Here, we explored the function of intestinal microbes of Eospalax cansus and Eospalax rothschildi based on metagenomics.<br><br>RESULTS: Both zokor species have similar intestinal microbial composition, but E. cansus has a higher proportion of bacteria involved in carbohydrate degradation. Functional analysis based on KEGG and CAZy databases indicated that the intestinal microbes of E. cansus harboured stronger carbohydrate degradation ability, mainly in starch and sucrose metabolism, and further in cellulose degradation. Furthermore, the cellulase activity was significantly higher in E. cansus than that in E. rothschildi. Eospalax cansus has a stronger microbial fermentation ability due to an increase in fibre-degrading bacteria like unclassified_f_Lachnospiraceae, Ruminococcus, and Clostridium. In addition, the dominant bacteria isolated from zokor were Bacillus, some of which could degrade both cellulose and hemicellulose.<br><br>CONCLUSION: Metagenomic analysis and bacterial isolation experiments indicate that E. cansus has a stronger microbial cellulose-degrading capacity, possibly as an adaptation to its limited food resources underground. &#xa9; 2024 Society of Chemical Industry.},
}
@article {pmid39628067,
year = {2024},
author = {Fujimoto, S and Hatano, K and Banno, E and Motooka, D and De Velasco, MA and Kura, Y and Toyoda, S and Hashimoto, M and Adomi, S and Minami, T and Yoshimura, K and Oka, T and Hata, J and Matsushita, M and Takao, T and Takada, S and Tsujimura, A and Kojima, Y and Obara, W and Nakamura, S and Uemura, H and Nonomura, N and Fujita, K},
title = {Comparative analysis of gut microbiota in hormone-sensitive and castration-resistant prostate cancer in Japanese men.},
journal = {Cancer science},
volume = {},
number = {},
pages = {},
doi = {10.1111/cas.16408},
pmid = {39628067},
issn = {1349-7006},
support = {//Yakult Bio-Science Foundation/ ; //The Japanese Foundation for Prostate Research (JFPR)/ ; //The Japanese Urological Association/ ; },
abstract = {Gut microbiota plays a crucial role in the development and progression of prostate cancer, with previous studies indicating that certain bacterial taxa are more abundant in castration-resistant prostate cancer (CRPC) compared to hormone-sensitive prostate cancer (HSPC). Notably, the composition of gut microbiota can vary significantly by geographic region, and Japanese individuals have a distinct microbial profile. However, research exploring these differences within Japanese populations remains limited. This study investigated the gut microbiota differences between Japanese men with HSPC and CRPC and further validated these findings using a transgenic mouse model. Rectal swab samples were collected from 140 Japanese men diagnosed with HSPC (n = 84) or CRPC (n = 56) between September 2020 and July 2022. Gut microbiota composition was analyzed using 16S rRNA gene sequencing. Additionally, Pten-KO mice, which model the progression from HSPC to CRPC, underwent similar microbiota analysis. Results revealed significant differences in gut microbiota composition between HSPC and CRPC patients. Specifically, the CRPC group showed a higher abundance of Firmicutes, including Gemella and Lactobacillus, compared to the HSPC group. These differences were mirrored in the mouse model, where CRPC mice also showed an increase in these bacteria. This study identifies distinct microbial differences between HSPC and CRPC in Japanese men, suggesting that Gemella and Lactobacillus may be associated with the progression to castration resistance in prostate cancer. These findings suggest that gut microbiota differences may be associated with prostate cancer progression. Further research is needed to explore the potential of targeting the microbiota as a therapeutic strategy.},
}
@article {pmid39627869,
year = {2024},
author = {Richy, E and Thiago Dobbler, P and Tláskal, V and López-Mondéjar, R and Baldrian, P and Kyselková, M},
title = {Long-read sequencing sheds light on key bacteria contributing to deadwood decomposition processes.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {99},
pmid = {39627869},
issn = {2524-6372},
support = {CZ.02.01.01/00/22_008/0004635//Ministry of Education, Youth and Sports of the Czech Republic/ ; },
abstract = {BACKGROUND: Deadwood decomposition is an essential ecological process in forest ecosystems, playing a key role in nutrient cycling and carbon sequestration by enriching soils with organic matter. This process is driven by diverse microbial communities encompassing specialized functions in breaking down organic matter, but the specific roles of individual microorganisms in this process are still not fully understood.<br><br>RESULTS: Here, we characterized the deadwood microbiome in a natural mixed temperate forest in Central Europe using PacBio HiFi long-read sequencing and a genome-resolved transcriptomics approach in order to uncover key microbial contributors to wood decomposition. We obtained high quality assemblies, which allowed attribution of complex microbial functions such as nitrogen fixation to individual microbial taxa and enabled the recovery of metagenome-assembled genomes (MAGs) from both abundant and rare deadwood bacteria. We successfully assembled 69 MAGs (including 14 high-quality and 7 single-contig genomes) from 4 samples, representing most of the abundant bacterial phyla in deadwood. The MAGs exhibited a rich diversity of carbohydrate-active enzymes (CAZymes), with Myxococcota encoding the highest number of CAZymes and the full complement of enzymes required for cellulose decomposition. For the first time we observed active nitrogen fixation by Steroidobacteraceae, as well as hemicellulose degradation and chitin recycling by Patescibacteria. Furthermore, PacBio HiFi sequencing identified over 1000 biosynthetic gene clusters, highlighting a vast potential for secondary metabolite production in deadwood, particularly in Pseudomonadota and Myxococcota.<br><br>CONCLUSIONS: PacBio HiFi long-read sequencing offers comprehensive insights into deadwood decomposition processes by advancing the identification of functional features involving multiple genes. It represents a robust tool for unraveling novel microbial genomes in complex ecosystems and allows the identification of key microorganisms contributing to deadwood decomposition.},
}
@article {pmid39627685,
year = {2024},
author = {Bradford, LM and Carrillo, C and Wong, A},
title = {Managing false positives during detection of pathogen sequences in shotgun metagenomics datasets.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {372},
pmid = {39627685},
issn = {1471-2105},
support = {OAF-2020-101088//Ontario Ministry of Agriculture, Food, and Rural Affairs (OMAFRA)/ ; },
mesh = {*Metagenomics/methods ; *Salmonella/genetics ; *Software ; False Positive Reactions ; Sensitivity and Specificity ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; Food Microbiology/methods ; },
abstract = {BACKGROUND: Culture-independent diagnostic tests are gaining popularity as tools for detecting pathogens in food. Shotgun sequencing holds substantial promise for food testing as it provides abundant information on microbial communities, but the challenge is in analyzing large and complex sequencing datasets with a high degree of both sensitivity and specificity. Falsely classifying sequencing reads as originating from pathogens can lead to unnecessary food recalls or production shutdowns, while low sensitivity resulting in false negatives could lead to preventable illness.<br><br>RESULTS: We used simulated and published shotgun sequencing datasets containing Salmonella-derived reads to explore the appearance and mitigation of false positive results using the popular taxonomic annotation softwares Kraken2 and Metaphlan4. Using default parameters, Kraken2 is sensitive but prone to false positives, while Metaphlan4 is more specific but unable to detect Salmonella at low abundance. We then developed a bioinformatic pipeline for identifying and removing reads falsely identified as Salmonella by Kraken2 while retaining high sensitivity. Carefully considering software parameters and database choices is essential to avoiding false positive sample calls. With well-chosen parameters plus additional steps to confirm the taxonomic origin of reads, it is possible to detect pathogens with very high specificity and sensitivity.},
}
@article {pmid39626922,
year = {2024},
author = {Vasudevan, HN and Lazar, AA and Reyes, K and Rong, DA and Arevalo, S and Federman, S and Chan, JW and Chiu, CY and Miller, S and Yom, SS},
title = {Comparison of Plasma Metagenomic Next-generation Sequencing and PCR Methods for Epstein-Barr Virus Viral Load Monitoring in Nasopharyngeal Carcinoma.},
journal = {Anticancer research},
volume = {44},
number = {12},
pages = {5445-5453},
doi = {10.21873/anticanres.17370},
pmid = {39626922},
issn = {1791-7530},
mesh = {Humans ; *Herpesvirus 4, Human/genetics/isolation &amp; purification ; *Viral Load ; *Nasopharyngeal Carcinoma/virology/blood/diagnosis ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; *Metagenomics/methods ; Middle Aged ; *Epstein-Barr Virus Infections/virology/blood/diagnosis ; *Polymerase Chain Reaction/methods ; *Nasopharyngeal Neoplasms/virology/blood/diagnosis ; Adult ; Aged ; DNA, Viral/blood/genetics ; },
abstract = {BACKGROUND/AIM: Plasma Epstein-Barr virus (EBV) viral load measurement is prognostic in nasopharyngeal carcinoma (NPC) disease monitoring; however, a consensus measurement approach does not exist. This study characterized the clinical performance of metagenomic next-generation sequencing (mNGS), an unbiased sequencing-based assay distinct from polymerase chain reaction (PCR) or targeted sequencing approaches, in 73 peripheral blood specimens from 32 patients diagnosed with NPC.<br><br>PATIENTS AND METHODS: Samples were analyzed for plasma EBV viral load either by mNGS profiling or PCR-based assays (either LMP2 or BAMHI-W PCR) and compared to tumor presence by clinical assessment. Plasma mNGS-based EBV detection was quantified as reads per million (RPM).<br><br>RESULTS: Plasma mNGS displayed similar overall performance (100% sensitivity, 86% specificity, 92% accuracy) to BAMHI-W PCR (100% sensitivity, 86% specificity, 94% accuracy) and superior performance to the LMP2 PCR assay (36% sensitivity, 56% specificity, 45% accuracy). In a subset of 13 patients who underwent longitudinal analysis, plasma mNGS EBV RPM correlated with cancer recurrence (95%CI Pre-CRT=232.10&#xb1;214; 95%CI Post-CRT=0.34&#xb1;0.32; 95%CI difference=-231.70&#xb1;214; *p=0.03, paired t-test), suggesting plasma mNGS exhibits potential for monitoring recurrence.<br><br>CONCLUSION: Plasma mNGS is a distinct method for EBV titer measurement in NPC patients and more broadly, is a promising method for non-invasive monitoring of disease status for infection-associated malignancies.},
}
@article {pmid39626557,
year = {2024},
author = {Peng, Q and Cheng, S and Huang, X and Pu, Y and Xie, G},
title = {Comprehensive multi-omics analysis of fermented Chinese artichoke: Insights from Flavoromics, metagenomics, and untargeted metabolomics.},
journal = {Food chemistry},
volume = {467},
number = {},
pages = {142278},
doi = {10.1016/j.foodchem.2024.142278},
pmid = {39626557},
issn = {1873-7072},
abstract = {Fermented Chinese Artichoke, a traditional Chinese fermented vegetable, has a distinctive flavor profile shaped by its fermentation process. This study applied flavoromics, metagenomics, and untargeted metabolomics to comprehensively analyze flavor compounds, microbial communities, and metabolic transformations during fermentation. We identified 43 volatile organic compounds (VOCs), with Terpineol, 1-Hexanol, and Linalool as the predominant components. Metagenomic analysis highlighted Lactiplantibacillus plantarum, Priestia megaterium, and Pediococcus pentosaceus as the dominant species, while Lactiplantibacillus, Pediococcus, and Bacillus were key in flavor development. Untargeted metabolomics further revealed increases in organic acids, amino acids, and umami compounds, contributing to flavor enhancement. These findings offer valuable insights into flavor formation mechanisms in Fermented Chinese Artichoke and provide guidance for improving its industrial fermentation quality.},
}
@article {pmid39628520,
year = {2023},
author = {Li, L},
title = {Next-generation synthetic biology approaches for the accelerated discovery of microbial natural products.},
journal = {Engineering microbiology},
volume = {3},
number = {1},
pages = {100060},
pmid = {39628520},
issn = {2667-3703},
abstract = {Microbial natural products (NPs) and their derivates have been widely used in health care and agriculture during the past few decades. Although large-scale bacterial or fungal (meta)genomic mining has revealed the tremendous biosynthetic potentials to produce novel small molecules, there remains a lack of universal approaches to link NP biosynthetic gene clusters (BGCs) to their associated products at a large scale and speed. In the last ten years, a series of emerging technologies have been established alongside the developments in synthetic biology to engineer cryptic metabolite BGCs and edit host genomes. Diverse computational tools, such as antiSMASH and PRISM, have also been simultaneously developed to rapidly identify BGCs and predict the chemical structures of their products. This review discusses the recent developments and trends pertaining to the accelerated discovery of microbial NPs driven by a wide variety of next-generation synthetic biology approaches, with an emphasis on the in situ activation of silent BGCs at scale, the direct cloning or refactoring of BGCs of interest for heterologous expression, and the synthetic-bioinformatic natural products (syn-BNP) approach for the guided rapid access of bioactive non-ribosomal peptides.},
}
@article {pmid39626551,
year = {2024},
author = {Xu, C and Han, A and Tian, Y and Sun, S},
title = {Based on computer simulation and experimental verification: mining and characterizing novel antimicrobial peptides from soil microbiome.},
journal = {Food chemistry},
volume = {467},
number = {},
pages = {142275},
doi = {10.1016/j.foodchem.2024.142275},
pmid = {39626551},
issn = {1873-7072},
abstract = {Antimicrobial peptides (AMPs) show great promise for enhancing food safety and extending shelf life, but traditional screening methods are complex and costly. To address these issues, we developed a deep learning-based prediction pipeline to identify potential AMPs from soil metagenomic data, achieving high accuracy (92.71 %) and precision (91.29 %). Based on model scoring, surface charge, and Hemopred and ToxinPred screenings, we identified nine candidate peptides. Peptide P4 (GTAWRWHYRARS) showed the best binding affinity to MrkH in molecular docking studies and was validated through molecular dynamics simulations. The chemically synthesized P4 demonstrated significant antimicrobial activity against Klebsiella pneumoniae, Escherichia coli, and Staphylococcus aureus, indicating its potential as an effective alternative to traditional food antimicrobial agents. This study highlights the effectiveness of our integrated prediction pipeline for discovering new AMPs.},
}
@article {pmid39626421,
year = {2024},
author = {Wang, J and Wu, D and Wu, Q and Chen, J and Zhao, Y and Wang, H and Liu, F and Yuan, Q},
title = {Vertical profiles of community and activity of methanotrophs in large lake and reservoir of Southwest China.},
journal = {The Science of the total environment},
volume = {957},
number = {},
pages = {177782},
doi = {10.1016/j.scitotenv.2024.177782},
pmid = {39626421},
issn = {1879-1026},
abstract = {Microbial methane oxidation plays a significant role in regulating methane emissions from lakes and reservoirs. However, the differences in methane oxidation activity and methanotrophic community between lakes and reservoirs remain inadequately characterized. In this study, sediment and water samples were collected from the large shallow lake (Dianchi) and deep reservoirs (Dongfeng and Hongjiadu) located in karst area, Southwest China. The results indicated that the rates of aerobic oxidation of methane (AeOM) in lake sediment ranged from 7.1 to 27.7 μg g[-1] d[-1], which was higher than that in reservoirs sediment (1.92 to 11.56 μg g[-1] d[-1]). Similarly, the average AeOM in the water column of lake (104.7 μg L[-1] d[-1]) was much higher than that of reservoirs (46 μg L[-1] d[-1]). The content of sediment organic carbon and dissolved inorganic carbon were important factors that influenced the rates of AeOM in sediment and water column, respectively. 16S rRNA genes sequencing revealed a higher relative abundance of methanotrophs in lake sediments compared to reservoir sediments. The dominant methanotrophic taxa in lake was Methylococcaceae (type Ib), while Methylomonadaceae (type Ia) was predominant in reservoirs. Meanwhile, anaerobic methane-oxidizing microorganisms Candidatus Methylomirabilis and Candidatus Methanoperedens were also abundant in sediments of reservoirs. However, metatranscriptomic analysis revealed that the type I methanotrophs, especially Methylobacter, was most active in the sediment of both lake and reservoir. Water depth and conductivity could be the key controlling factors of the structures of methanotrophic communities in sediment and water column, respectively. Metagenome-assembled genomes suggested that type I methanotrophs exhibited greater motility, as evidenced by a higher number of flagellar assembly genes, while type II methanotrophs demonstrated advantages in metabolic processes such as carbon, phosphorus, and methane metabolism.},
}
@article {pmid39626398,
year = {2024},
author = {Song, A and Si, Z and Xu, D and Wei, B and Wang, E and Chong, F and Fan, F},
title = {Lanthanum and cerium added to soil influence microbial carbon and nitrogen cycling genes.},
journal = {Journal of environmental management},
volume = {373},
number = {},
pages = {123509},
doi = {10.1016/j.jenvman.2024.123509},
pmid = {39626398},
issn = {1095-8630},
abstract = {The soil microbiome plays an important role in carbon (C) and nitrogen (N) processing and storage and is influenced by rare earth elements (REEs), which can have both direct and indirect effects on plant metabolic processes. Using conventional physicochemical methods and metagenomic-based analyses, we investigated REEs effects on soil respiration, soil mineral N, soil microbial community structure and functional genes related to C and N metabolism. High doses of cerium (0.16 and 0.32 mmol kg[-1] soil) increased CO2 net production rate by 59 and 42%, and N2O net production rate by 255 and 609%, respectively, compared to no REEs. Similarly, high doses of lanthanum (0.16 and 0.32 mmol kg[-1] soil) increased CO2 net production rate by 47 and 39%, and N2O net production rate by 105 and 187%, respectively. Increased soil respiration from altered relative abundances of key soil microorganisms associated with soil N cycling and organic matter degradation and functional genes encoding enzymes involved in C and N metabolism, accelerated N mineralization. Elevated REEs levels substantially increased the relative abundances of functional genes related to cellulose, chitin, glucans, hemicellulose, lignin, and peptidoglycan degradation. REEs also influenced multiple functional genes associated with the N cycle. The abundance of genes responsible for organic N degradation and synthesis, such as asnB, gdh_K15371, glsA, and gs, increased with elevated cerium and lanthanum concentrations. Similarly, the abundances of denitrification genes, including narl, narJ, narZ, and nosZ, also rose with increasing amounts of cerium and lanthanum. However, the decrease in narB and nirB gene abundance with increasing REE concentrations was attributed to the reduction of nitrate to amino groups. Our findings highlight the influence of REEs on key soil microorganisms associated with soil N cycling and organic matter degradation and key functional genes in soil C and N metabolism, with implications for agriculture, environmental protection, and human health.},
}
@article {pmid39626197,
year = {2024},
author = {Jéglot, A and Sanchez-Cid, C and Sørensen, SR and Schnorr, KM and Plauborg, F and Vogel, TM and Elsgaard, L},
title = {Bacterial bioaugmentation of woodchip bioreactors to increase nitrate removal in cold agricultural drainage water.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/09593330.2024.2432483},
pmid = {39626197},
issn = {1479-487X},
abstract = {Woodchip bioreactors (WBRs) are biological systems designed to prevent excess nitrate (NO3[-]) leaching from agricultural fields to aquatic ecosystems. Nitrate is removed by microbial denitrification, but the enzyme-mediated process slows down at cold temperatures (<10°C), where NO3[-] removal in WBRs can be less than 20%. We studied the use of bacterial bioaugmentation in replicated test-scale WBRs (∼0.1 m[3]) as an environmental technology to increase NO3[-] removal at cold temperatures. Nitrate removal rates increased following injection of a nitrate-reducing inoculum (Pseudomonas proteolytica and Klebsiella sp.), but the effect disappeared within a week and was reproduced in control WBRs by injection of sterile medium (phosphate buffer saline). Metagenome analyses showed a shift in the bacterial community composition after bioaugmentation in the planktonic phase of the woodchip reactors, but not in the solid phase (woodchip matrix). Only in the planktonic phase, Pseudomonas and Klebsiella increased their relative abundance as monitored by 16S rRNA gene sequences. In addition, an increased abundance of genes related to NO3[-] transformation after bacterial inoculation was observed in the metagenomic sequences. After one week, bacterial community composition became similar to its initial state, indicating resilience of the WBR microbial communities. We conclude that improved inoculation methods are needed to unlock the potential of bioaugmentation to increase NO3[-] removal at cold temperatures and make it a relevant technology for practical use at field-scale.},
}
@article {pmid39625881,
year = {2024},
author = {Sun, B and Guo, J and Jin, H and Jin, Z and Sun, Y and Mao, Y and Xie, F and He, Y and Sun, Z and Li, W and Ivanov, I and Tian, H},
title = {MetaCONNET: A metagenomic polishing tool for long-read assemblies.},
journal = {PloS one},
volume = {19},
number = {12},
pages = {e0313515},
doi = {10.1371/journal.pone.0313515},
pmid = {39625881},
issn = {1932-6203},
mesh = {*Metagenomics/methods ; *Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Software ; Animals ; Deep Learning ; },
abstract = {Accurate and high coverage genome assemblies are the basis for downstream analysis of metagenomic studies. Long-read sequencing technology is an ideal tool to facilitate the assemblies of metagenome, except for the drawback of usually producing reads with high sequencing error rate. Many polishing tools were developed to correct the sequencing error, but most are designed on the ground of one or two species. Considering the complexity and uneven depth of metagenomic study, we present a novel deep-learning polishing tool named MetaCONNET for polishing metagenomic assemblies. We evaluate MetaCONNET against Medaka, CONNET and NextPolish in accuracy, coverage, contiguity and resource consumption. Our results demonstrate that MetaCONNET provides a valuable polishing tool and can be applied to many metagenomic studies.},
}
@article {pmid39625614,
year = {2024},
author = {Saeng-Kla, K and Mhuantong, W and Termsaithong, T and Pinyakong, O and Sonthiphand, P},
title = {Biodegradation of Di-2-Ethylhexyl Phthalate by Mangrove Sediment Microbiome Impacted by Chronic Plastic Waste.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {27},
number = {1},
pages = {19},
pmid = {39625614},
issn = {1436-2236},
support = {FF-072/2567//Mahidol University (Fundamental Fund: fiscal year 2024 by National Science Research and Innovation Fund (NSRF)/ ; },
mesh = {*Diethylhexyl Phthalate/metabolism ; *Geologic Sediments/microbiology ; *Biodegradation, Environmental ; *Microbiota ; Water Pollutants, Chemical/metabolism ; Plastics/metabolism ; Gordonia Bacterium/metabolism/genetics ; Plasticizers/metabolism ; Wetlands ; Bacteria/metabolism/classification/genetics/isolation &amp; purification ; },
abstract = {Plastic pollution through the leaching of di(2-ethylhexyl) phthalate (DEHP), a widely used plasticizer, has led to the emergence of mangrove pollution. This study aimed to assess the DEHP removal efficiency of indigenous mangrove sediment microbiomes and identify key DEHP degraders using microcosm construction and metagenomic analysis. During the 35-day incubation period, the indigenous mangrove sediment microbiome, affected by chronic plastic pollution, demonstrated a 99% degradation efficiency of 200 mg/kg DEHP. Spearman's correlation analysis suggested that Myxococcales, Methyloligellaceae, Mycobacterium, and Micromonospora were potentially responsible for DEHP degradation. Based on PICRUSt2, the DEHP-degrading pathway in the sediment was predicted to be an anaerobic process involving catechol metabolism through catC, pcaD, pcaI, pcaF, and fadA. Efficient bacterial isolates from the mangrove sediment, identified as Gordonia sp. and Gordonia polyisoprenivorans, were able to degrade DEHP (65-97%) within 7 days and showed the ability to degrade other phthalate esters (PAEs).},
}
@article {pmid39624724,
year = {2024},
author = {Liu, Z and Yin, Q and Fang, Y and Zhang, X and Xia, W and Jiao, Z and Song, T and Wan, H and Guo, T},
title = {Effect of exogenous thermophilic biocontrol agent inoculum on the high temperature chicken manure composting.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1484047},
pmid = {39624724},
issn = {1664-302X},
abstract = {INTRODUCTION: Aerobic composting is an effective method for utilizing chicken manure. However, its low carbon to nitrogen (C/N) ratio leads to slow heating and short high-temperature phases, which reduce composting efficiency and product quality.<br><br>METHODS: To address this issue, splinted mushroom cultivation residues were added to adjust the C/N ratio, and exogenous thermophilic composting strains were introduced to increase composting temperature. This study analyzed the relationship between physicochemical metabolites and microbial community structure during high-temperature chicken manure composting.<br><br>RESULTS AND DISCUSSION: Based on metagenomic and physicochemical analyses, results showed that the exogenous microbial agents extended the thermophilic phase by three-times, reduced the heating phase duration by 75%, and increased nitrogen, phosphorus, potassium, and soluble organic carbon contents by 3.61, 21.63, 7.21, and 39.03%, respectively. Genes associated with amino acid metabolism were significantly enriched during the heating phase, while genes involved in the tricarboxylic acid cycle were more active in the thermophilic phase. During the thermophilic phase, bacterial diversity and richness decreased compared to the heating and cooling phases. Functional microbes such as Bacillus, Caldicoprobacter, and Virgibacillus showed a positive correlation with the key differential metabolites. While Actinomadura, Saccharomonospora, Paenibacillus, and Aneurinibacillus displayed an opposite correlation. Further experiments demonstrated that the increased temperature during the thermophilic phase triggered the upregulation of oleic acid metabolism and piperidine metabolism pathways in functional microorganisms, leading to the production of heat stabilizers and protective agents like oleic acid, gallic acid, and 2-piperidone. This phenomenon helped maintain microbial viability during the thermophilic phase and improved composting efficiency.},
}
@article {pmid39624721,
year = {2024},
author = {Liu, C and Dan, H and Yang, Y and Du, Y and Hao, Z and Chen, L and Zhu, K and Liu, B and Niu, L and Zhao, Y and Wang, Y and Shen, L and Gan, M and Zhu, L},
title = {Enhanced immunity: the gut microbiota changes in high-altitude Tibetan pigs compared to Yorkshire pigs.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1469253},
pmid = {39624721},
issn = {1664-302X},
abstract = {INTRODUCTION: Long-term domestication in high-altitude environments has led to unique changes in the gut microbiota of Tibetan Pigs. This study aims to investigate specific alterations in the intestinal flora of Tibetan Pigs compared to Yorkshire pigs.<br><br>METHODS: We employed 16S rRNA and metagenomic sequencing technologies for comprehensive analysis of the gut microbiota. The data collected allowed us to assess microbial community structures and functional capabilities.<br><br>RESULTS: Our analysis revealed that Tibetan Pigs raised under a "free-range + supplementary feeding" model exhibited increased abundance of microbial communities associated with short-chain fatty acid synthesis and the digestion of cellulose and hemicellulose. Notably, the characteristic bacterium Rhodococcus, commonly found in high-altitude environments, was enriched in the gut microbiota of Tibetan Pigs, facilitating the efficient utilization of natural compounds and degradation of toxic substances. Additionally, the increased abundance of probiotics in these pigs enhances their immunity, which may involve mechanisms such as disrupting the structure of pathogenic bacteria and detoxifying harmful metabolites.<br><br>DISCUSSION: These findings underscore the advantages of Tibetan Pigs over common commercial breeds, highlighting their unique gut microbiota adaptations. Furthermore, they open new avenues for screening potential probiotics and developing genetic breeding strategies for improved livestock varieties.<br><br>CONCLUSION: Understanding the distinct gut microbiota of Tibetan Pigs provides valuable insights into their health benefits and resilience, contributing to future research on breed improvement and microbiome applications in agriculture.},
}
@article {pmid39624636,
year = {2024},
author = {Huang, H and Liu, Y and Liu, Y and Lin, J and Guo, H and Xu, Q and Zhang, H and Li, Z and Zhu, H and Ding, M},
title = {Analysis and Perception of Chlamydia psittaci Pneumonia: Novel Insights of the Rare Disease in Infectiology.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {5261-5275},
pmid = {39624636},
issn = {1178-6973},
abstract = {OBJECTIVE: To investigate and analyze the clinical features, diagnosis and treatment, and prognosis of rare Chlamydia psittaci pneumonia, and to improve the understanding of this rare disease.<br><br>METHODS: A retrospective analysis and exploration was performed for 33 cases of patients with Chlamydia psittaci pneumonia in the First Affiliated Hospital of Gannan Medical University from January 2017 to March 2024, and the clinical features, diagnosis, treatment and key points for differential diagnosis were summarized and analyzed. Meanwhile, the latest literature from PubMed was retrieved to systematically discuss the research progress in Chlamydia psittaci pneumonia.<br><br>RESULTS: A total of 33 patients with Chlamydia psittaci pneumonia were included in this study, including 21 males (63.64%) and 12 females (36.36%), with a median age of 59 (32-79) years. There were 27 cases (81.82%) of patients accompanied with a history of poultry contact, 22 patients (66.67%) had underlying diseases. In our study, patients with Chlamydia psittaci pneumonia were mainly affected in Autumn (21.21%) and Winter (54.55%). All patients had undergone bronchoscopy and obtained bronchoalverolar lavage fluid (BALF) for metagenomic next-generation sequencing (mNGS) detection, and mNGS results showed that all patients (100%) were co-infected with multiple pathogens including Chlamydia psittaci. All patients were given antimicrobial therapy after diagnosis, and no treatment-related adverse reactions or adverse events were observed in our study, the average length of hospitalization was 11.09 days. Fortunately, no death was observed in our study, and patients were all discharged from hospital after recovery and in favourable physical and psychological conditions after discharge.<br><br>CONCLUSION: Chlamydia psittaci pneumonia lacks specific clinical features or manifestations and tends to develop into severe exacerbation. mNGS could help to achieve an accurate diagnosis. Early administration of antibiotics can improve the prognosis of patients to the greatest extent.},
}
@article {pmid39624158,
year = {2024},
author = {Jimenez-Lopez, O and Ray, T and Dean, C and Slizovskiy, I and Deere, J and Wolf, T and Moore, S and Primus, A and Høy-Petersen, J and Finstad, S and Mo, J and Sørum, H and Noyes, N},
title = {The gut microbiome and resistome of yellow perch (Perca flavescens) living in Minnesota lakes under varying anthropogenic pressure.},
journal = {One health (Amsterdam, Netherlands)},
volume = {19},
number = {},
pages = {100933},
pmid = {39624158},
issn = {2352-7714},
abstract = {Anthropogenic activities can significantly impact wildlife in natural water bodies, affecting not only the host's physiology but also its microbiome. This study aimed to analyze the gut microbiome and antimicrobial resistance gene profile (i.e., the resistome) of yellow perch living in lakes subjected to different levels of anthropogenic pressure: wastewater effluent-impacted lakes and undeveloped lakes. Total DNA and RNA from gut content samples were extracted and sequenced for analysis. Results indicate that the gut resistome and microbiome of yellow perch differ between lakes, perhaps due to varying anthropogenic pressure. The resistome was predominated by macrolide resistance genes, particularly the MLS23S group, making up 53 % of resistome sequences from effluent-impacted lakes and 73 % from undeveloped lakes. The colistin resistance gene group (mcr) was detected in numerous samples, including variants associated with Aeromonas and the family Enterobacteriaceae. The gut microbiome across all samples was dominated by the phyla Proteobacteria, Firmicutes, and Actinobacteria, with the opportunistic pathogens Plesiomonas shigelloides and Aeromonas veronii more abundant in effluent-impacted lakes. Metagenomic analysis of wild fish samples offers valuable insights into the effects of anthropogenic pressures on microbial communities, including antimicrobial resistance genes, in water bodies.},
}
@article {pmid39624075,
year = {2024},
author = {Chen, X and Zheng, H and Wang, T and Feng, Z and Wang, J and Liu, Y and Qin, W and Kong, F and Qin, X},
title = {Early Hints of Metagenome Next-Generation Sequencing and Copy Number Variations Analysis: An Occult Case of Leptomeningeal Metastasis With Rapid Cognitive Decline.},
journal = {Clinical case reports},
volume = {12},
number = {12},
pages = {e9676},
pmid = {39624075},
issn = {2050-0904},
abstract = {Early detection and treatment are critical for improving the prognosis of patients with leptomeningeal metastasis. However, heterogeneous clinical manifestations, non-specific imaging, and limited sensitivity of cerebrospinal fluid cytology posed challenges to identifying leptomeningeal metastasis in the early stage. Here we reported a case of lung adenocarcinoma complaining of rapid cognitive decline, whose magnetic resonance imaging showed interstitial brain edema. Under the circumstances of negative cerebrospinal fluid cytology, metagenome next-generation sequencing and copy number variations analysis were applied, which indicated leptomeningeal metastasis and was confirmed in the subsequent cytology.},
}
@article {pmid39624039,
year = {2024},
author = {Sha, J and Shao, J and Lu, S and Zhang, M and Gu, C and Deng, Y and Zhang, J and Feng, Y},
title = {A case report of severe pneumonia caused by Aeromonas dhakensis infection complicated with severe atrial septal defect.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1476864},
pmid = {39624039},
issn = {2296-858X},
abstract = {Aeromonas dhakensis is an increasingly recognized human pathogen in recent years and was first isolated and reported in a sample of childhood diarrhea in Bangladesh. More and more cases of Aeromonas dhakensis infection have been reported in recent years. Here we report a case of severe pneumonia caused by Aeromonas dhakensis with severe atrial septal defect. The patient, a 56-year-old male, was admitted to the hospital with severe hypoxemia and severe septic shock. Detection of the patient's bronchoalveolar lavage fluid (BALF) and peripheral blood by the metagenomic next generation sequencing (mNGS) indicated Aeromonas dhakensis infection.},
}
@article {pmid39623774,
year = {2024},
author = {Hu, Y and Wang, ML and Yang, RL and Shao, ZK and Du, YH and Kang, Y and Zhu, YX and Xue, XF},
title = {Symbiotic bacteria play crucial roles in a herbivorous mite host suitability.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.8571},
pmid = {39623774},
issn = {1526-4998},
support = {//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The tomato russet mite (TRM), Aculops lycopersici, is a strictly herbivorous and economically significant pest that infests Solanaceae plants, but its host suitability varies, showing high performance on tomatoes. Although symbiotic bacteria have been suggested to play crucial roles in the host adaptation of herbivores, their effects on TRM remain unclear.<br><br>RESULTS: In this study, using next generation high-throughput sequencing of the bacterial 16S rRNA data, we identified the bacterial diversity and community composition of TRM feeding on tomato, eggplant, and chili. Our results show no significant difference in the bacterial community composition of TRM across three host plants. However, the relative density of Escherichia coli (TRM_Escherichia) showed 9.36-fold higher on tomato than on eggplant and chili. These results align with the observed TRM performance among three host plants. When TRM_Escherichia was reduced using antibiotics, the treated TRM decreased the population density on tomato. However, when we transferred TRM from eggplant to tomato, the population density of TRM increased, coinciding with an increase of the TRM_Escherichia density. These results indicate that TRM_Escherichia may affect the host suitability of TRM. Our fluorescence in situ hybridization (FISH) results further showed that TRM_Escherichia is primarily distributed in the salivary glands. Metagenomic data results suggest that TRM_Escherichia functions in food digestion and energy metabolism.<br><br>CONCLUSION: We provided the first comprehensive analysis of TRM bacterial communities. Our findings demonstrate that the symbiotic bacterium TRM_Escherichia may play crucial roles in the suitability of TRM feeding on different Solanaceae hosts. &#xa9; 2024 Society of Chemical Industry.},
}
@article {pmid39623670,
year = {2024},
author = {Babady, NE and Chiu, CY and Craney, A and Gaston, DC and Hicklen, RS and Hogan, CA and John, TM and Stewart, AG},
title = {Diagnosis and management of invasive fungal diseases by next-generation sequencing: are we there yet?.},
journal = {Expert review of molecular diagnostics},
volume = {},
number = {},
pages = {},
doi = {10.1080/14737159.2024.2436396},
pmid = {39623670},
issn = {1744-8352},
abstract = {INTRODUCTION: Invasive fungal diseases (IFDs) are a serious threat to immunocompromised patients. Routine diagnostic methods have limited performance in identifying IFDs. Next-generation sequencing (NGS) including metagenomic NGS (mNGS) and whole genome sequencing (WGS) recently emerged as diagnostic methods that could provide more accurate and timely diagnoses and management of IFDs.<br><br>AREAS COVERED: This article describes the emergence of NGS as a diagnostic tool to address the limitations of current tests. The literature regarding its application and clinical utility in the diagnosis of IFDs is reviewed. Practical considerations, challenges, and opportunities as they relate to the development and implementation of mNGS and WGS for fungal pathogens are discussed.<br><br>EXPERT OPINION: NGS emerged over a decade ago with the potential to solve many of the challenges in diagnosing infectious diseases, including IFDs. However, published literature has yielded conflicting data about its clinical utility. The increased clinical adoption of NGS is improving our understanding of how to interpret and use its results to guide actionable decisions. Still, several gaps remain. As the cost, effort, and expertise involved in performing NGS decrease and the reporting of its results becomes standardized, NGS is poised to fill current gaps in the diagnosis of IFDs.},
}
@article {pmid39623529,
year = {2024},
author = {Ma, J and Sun, S and Cheng, X and Meng, C and Zhao, H and Fu, W and Gao, Y and Ma, L and Yang, Z and Yao, H and Su, J},
title = {Unraveling the role of gut microbiome in predicting adverse events in neoadjuvant therapy for rectal cancer.},
journal = {Human vaccines &amp; immunotherapeutics},
volume = {20},
number = {1},
pages = {2430087},
doi = {10.1080/21645515.2024.2430087},
pmid = {39623529},
issn = {2164-554X},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Neoadjuvant Therapy/adverse effects/methods ; Male ; Female ; Middle Aged ; *Rectal Neoplasms/therapy/microbiology ; Aged ; *Feces/microbiology ; Metabolomics ; Metabolome ; Immunotherapy/methods/adverse effects ; Adult ; Chemoradiotherapy/adverse effects/methods ; Metagenomics/methods ; },
abstract = {Some patients may develop adverse events during neoadjuvant chemoradiotherapy combined with immunotherapy, influencing response rates. The roles of intestinal microbiome and its metabolites in therapeutic adverse events remain unclear. We collected baseline fecal samples from 21 patients with adverse events (AE group) and 11 patients without adverse events (Non-AE group). Their microbiota and metabolome were characterized using metagenomic shotgun sequencing and untargeted metabolomics. At the species level, the gut microbiota in the Non-AE group exhibits significantly higher abundance of Clostridium sp. Alistipes sp. and lower abundance of Lachnoclostridium sp. Weissella cibaria, Weissella confusa, compared to the AE group (p < .05). A total of 58 discriminative metabolites were identified between groups. Beta-alanine metabolism was scattered. Boc-beta-cyano-L-alanine and CoQ9 were significantly increased in patients without adverse events, while linoleic acid increased in patients with adverse events. The increased Alistipes sp. in the Non-AE group was positively correlated with Boc-beta-cyano-L-alanine and negatively correlated with linoleic acid (p < .05). We constructed a combined microbiome-metabolite model to distinguish Non-AE and AE patients with an AUC of 0.963 via the random forest algorithm. Our findings provided a novel insight into the interplay of multispecies microbial cluster and metabolites of rectal patients with adverse events in neoadjuvant chemoradiotherapy combined with immunotherapy. These microbiota and metabolites deserve further investigations to reveal their roles in adverse events, providing clues for better treatment scenarios.Trial registration number: ClinicalTrials.gov identifier: NCT05368051.},
}
@article {pmid39623429,
year = {2024},
author = {Jiang, J and Wei, Y and Li, S and Mo, J and Li, X and Cao, M and Wang, H},
title = {Study on the application of microfluidic-based in vitro diagnostic technology in pathogenic detection of respiratory tract infections.},
journal = {Journal of translational medicine},
volume = {22},
number = {1},
pages = {1092},
pmid = {39623429},
issn = {1479-5876},
support = {2022PY026//Health Bureau of Zhejiang Province/ ; 2024KY44//Health Bureau of Zhejiang Province/ ; },
mesh = {Humans ; *Respiratory Tract Infections/microbiology/diagnosis ; *Microfluidics/methods ; Male ; Female ; Middle Aged ; *ROC Curve ; Adult ; Aged ; High-Throughput Nucleotide Sequencing ; Bronchoalveolar Lavage Fluid/microbiology ; Young Adult ; Adolescent ; },
abstract = {OBJECTIVE: To investigate the clinical application value of microfluidic-based in vitro diagnostic (IVD) technology in pathogenic detection of respiratory tract infections.<br><br>METHODS: A total of 300 clinical samples, including blood, bronchoalveolar lavage fluid, and pleural effusion, were collected from patients with respiratory tract infections. The samples were randomly divided into three groups: A, B, and C, with 100 cases in each group. Group A used traditional microbiological detection methods, Group B used metagenomic next-generation sequencing (mNGS) technology, and Group C used both microfluidic-based IVD technology and traditional microbiological detection methods to detect pathogenic microorganisms in the clinical samples. The positive detection rate, detection time, and detection cost were compared among the groups. The diagnostic performance of each group was compared using the Receiver Operating Characteristic (ROC) curve.<br><br>RESULTS: Traditional microbiological detection identified 38 positive samples (38%), including 45 pathogens; mNGS technology identified 95 positive samples (95%), including 210 pathogens; microfluidic-based IVD technology identified 96 positive samples (96%), including 158 pathogens. Microfluidic-based IVD technology had a significantly higher positive detection rate for pathogenic microorganisms compared to traditional culture techniques (96% vs 38%, &#x3c7;2&#x2009;=&#x2009;122.0, P&#x2009;<&#x2009;0.01), and it was also faster and cheaper than mNGS technology. ROC analysis showed that compared to traditional microbiological culture results, microfluidic-based IVD technology had significantly increased sensitivity and specificity, similar to mNGS technology.<br><br>CONCLUSION: In respiratory infectious diseases, microfluidic-based IVD technology had a higher detection rate for pathogenic microorganisms than traditional culture methods, and it had advantages in detection time and cost compared to mNGS technology. It could also detect critical drug-resistant genes of pathogens. Hence, microfluidic-based IVD technology can be a viable option for diagnosis and treatment of respiratory infectious diseases.},
}
@article {pmid39622769,
year = {2024},
author = {Ivan, FX and Tiew, PY and Jaggi, TK and Thng, KX and Pang, PH and Ong, TH and Abisheganaden, JA and Koh, MS and Chotirmall, SH},
title = {Sputum metagenomics reveals a multidrug resistant Pseudomonas-dominant severe asthma phenotype in an Asian population.},
journal = {Respirology (Carlton, Vic.)},
volume = {},
number = {},
pages = {},
doi = {10.1111/resp.14863},
pmid = {39622769},
issn = {1440-1843},
support = {AcRF Tier 1 Grant (RT1/22)//Singapore Ministry of Education/ ; MOH-000710//Singapore Ministry of Health's National Medical Research Council/ ; MOH-001275-00//Singapore Ministry of Health's National Medical Research Council/ ; MOH-001356//Singapore Ministry of Health's National Medical Research Council/ ; MOH-001636//Singapore Ministry of Health's National Medical Research Council/ ; },
abstract = {BACKGROUND AND OBJECTIVE: While the lung microbiome in severe asthma has been studied, work has employed targeted amplicon-based sequencing approaches without functional assessment with none focused on multi-ethnic Asian populations. Here we investigate the clinical relevance of microbial phenotypes of severe asthma in Asians using metagenomics.<br><br>METHODS: Prospective assessment of clinical, radiological, and immunological measures were performed in a multi-ethnic Asian severe asthma cohort (N&#x2009;=&#x2009;70) recruited across two centres in Singapore. Sputum was subjected to shotgun metagenomic sequencing and patients followed up for a 2-year period. Metagenomic assessment of sputum microbiomes, resistomes and virulomes were related to clinical outcomes.<br><br>RESULTS: The lung microbiome in a multi-ethnic Asian cohort with severe asthma demonstrates an increased abundance of Pseudomonas species. Unsupervised clustering of sputum metagenomes identified two patient clusters: C1 (n&#x2009;=&#x2009;52) characterized by upper airway commensals and C2 (n&#x2009;=&#x2009;18) dominated by established respiratory pathogens including M. catarrhalis, S. aureus and most significantly P. aeruginosa. C2 patients demonstrated a significantly increased exacerbation frequency on 2-year follow up and an antimicrobial resistome characterized by multidrug resistance. Virulomes appear indistinguishable between severe asthmatics with or without co-existing bronchiectasis, and C2 patients exhibit increased gene expression related to biofilm formation, effector delivery systems and microbial motility. Independent comparison of the C2 cluster to a non-asthmatic bronchiectasis cohort demonstrates analogous airway microbial virulence patterns.<br><br>CONCLUSION: Sputum metagenomics demonstrates a multidrug-resistant Pseudomonas-dominant severe asthma phenotype in Asians, characterized by poor clinical outcome including increased exacerbations which is independent of co-existing bronchiectasis.},
}
@article {pmid39622690,
year = {2024},
author = {Kim, S and Suh, DH and Lee, S and Kim, HS and Cho, SH and Woo, YR},
title = {Associations Between Skin Microbiome and Metabolome in the Pathogenesis of Atopic Dermatitis Patients With Scalp Involvement.},
journal = {Allergy, asthma &amp; immunology research},
volume = {16},
number = {6},
pages = {668-681},
doi = {10.4168/aair.2024.16.6.668},
pmid = {39622690},
issn = {2092-7355},
support = {2021R1I1A1A01052146/NRF/National Research Foundation of Korea/Korea ; },
abstract = {PURPOSE: Atopic dermatitis (AD) is a chronic inflammatory skin condition influenced by various factors, such as the skin microbiome and metabolome. However, specific contributions of these factors to scalp involvement in AD still need to be explored. In this study, we aimed to assess the associations between the skin microbiome and metabolome in AD patients with scalp dermatitis and healthy controls (HCs).<br><br>METHODS: A total of 20 AD patients with scalp involvement and 16 HCs were recruited, and their skin samples were collected for analysis. Bioinformatic analysis and 16S rRNA metagenomic sequencing were performed, with gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) conducted for AD-associated skin metabolites. Spearman correlation analysis was used to identify the correlations between AD-associated skin bacteria and metabolites.<br><br>RESULTS: The results revealed significant differences in bacterial taxa and metabolites between the lesional and non-lesional scalp skin samples of AD patients (groups LS and NL, respectively) and those of HCs (group HC). Notably, group LS showed a significantly increased relative abundance of the genus Staphylococcus and a decreased abundance of Cutibacterium compared to group HC. The reduced abundance of Cutibacterium was also observed when comparing LS to NL. The GC-TOF-MS analysis identified 33 significantly decreased metabolites and 17 significantly increased metabolites in groups LS and NL compared with group HC. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that amino acid-related metabolism was significantly altered in the metabolic pathway between groups LS, NL, and HC. Furthermore, Spearman correlation analysis showed significant correlations of the altered bacteria genera and skin metabolites between the 3 groups.<br><br>CONCLUSIONS: The results of this research provide valuable insights into the associations the skin microbiome and metabolome between groups LS, NL, and HC. Identifying these specific contributions may offer new avenues for understanding the pathogenesis of scalp involvement in AD patients and potentially lead to improving management strategies.},
}
@article {pmid39621710,
year = {2024},
author = {Mangoma, N and Zhou, N and Ncube, T},
title = {Metagenome-assembled genomes provide insight into the microbial taxonomy and ecology of the Buhera soda pans, Zimbabwe.},
journal = {PloS one},
volume = {19},
number = {12},
pages = {e0299620},
pmid = {39621710},
issn = {1932-6203},
mesh = {Zimbabwe ; *Metagenome ; *Phylogeny ; Metagenomics/methods ; Bacteria/genetics/classification ; Genome, Bacterial ; Ecosystem ; Microbiota/genetics ; Extreme Environments ; },
abstract = {The use of metagenomics has substantially improved our understanding of the taxonomy, phylogeny and ecology of extreme environment microbiomes. Advances in bioinformatics now permit the reconstruction of almost intact microbial genomes, called metagenome-assembled genomes (MAGs), from metagenomic sequence data, allowing for more precise cell-level taxonomic, phylogenetic and functional profiling of uncultured extremophiles. Here, we report on the recovery and characterisation of metagenome-assembled genomes from the Buhera soda pans located in eastern Zimbabwe. This ecosystem has not been studied despite its unique geochemistry and potential as a habitat for unique microorganisms. Metagenomic DNA from the soda pan was sequenced using the DNA Nanoball Sequencing (DNBSEQR) technique. Sequence analysis, done on the Knowledgebase (KBase) platform, involved quality assessment, read assembly, contig binning, and MAG extraction. The MAGs were subjected to taxonomic placement, phylogenetic profiling and functional annotation in order to establish their possible ecological roles in the soda pan ecosystem. A total of 16 bacterial MAGs of medium to high quality were recovered, all distributed among five phyla dominated by Pseudomonadota and Bacillota. Of the ten MAGs that were taxonomically classified up to genus level, five of them belonged to the halophilic/ haloalkaliphilic genera Alkalibacterium, Vibrio, Thioalkalivibrio, Cecembia and Nitrincola, underscoring the importance of haloalkaliphiles in the Buhera soda pans. Functional profiling revealed the possession of diverse carbohydrate-metabolising pathways by the MAGs, with glycolysis and the pentose phosphate pathways appearing to be key pathways in this ecosystem. Several MAGs possessed pathways that implicated them in some key aspects of the nitrogen and sulphur cycle. Some MAGs harboured both sulphate reduction and respiratory pathways, suggesting a possible mechanism of ATP biosynthesis through sulphate respiration. This study demonstrates the feasibility of the recovery and taxonomic and functional annotation of high quality microbial genomes from extreme environments, making it possible to establish the ecological roles and biotechnological potential of uncultured microorganisms.},
}
@article {pmid39269772,
year = {2024},
author = {Rahal, Z and Liu, Y and Peng, F and Yang, S and Jamal, MA and Sharma, M and Moreno, H and Damania, AV and Wong, MC and Ross, MC and Sinjab, A and Zhou, T and Chen, M and Tarifa Reischle, I and Feng, J and Chukwuocha, C and Tang, E and Abaya, C and Lim, JK and Leung, CH and Lin, HY and Deboever, N and Lee, JJ and Sepesi, B and Gibbons, DL and Wargo, JA and Fujimoto, J and Wang, L and Petrosino, JF and Ajami, NJ and Jenq, RR and Moghaddam, SJ and Cascone, T and Hoffman, K and Kadara, H},
title = {Inflammation Mediated by Gut Microbiome Alterations Promotes Lung Cancer Development and an Immunosuppressed Tumor Microenvironment.},
journal = {Cancer immunology research},
volume = {12},
number = {12},
pages = {1736-1752},
doi = {10.1158/2326-6066.CIR-24-0469},
pmid = {39269772},
issn = {2326-6074},
support = {R01 CA205608/CA/NCI NIH HHS/United States ; R01 CA248731/CA/NCI NIH HHS/United States ; R01CA248731//National Cancer Institute (NCI)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Tumor Microenvironment/immunology ; *Lung Neoplasms/immunology/microbiology/pathology ; Mice ; Humans ; *Inflammation/immunology ; Adenocarcinoma of Lung/immunology/microbiology/pathology ; Lipocalin-2/metabolism ; Mice, Inbred C57BL ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Mice, Knockout ; },
abstract = {Accumulating evidence indicates that the gut microbiome influences cancer progression and therapy. We recently showed that progressive changes in gut microbial diversity and composition are closely coupled with tobacco-associated lung adenocarcinoma in a human-relevant mouse model. Furthermore, we demonstrated that the loss of the antimicrobial protein Lcn2 in these mice exacerbates protumor inflammatory phenotypes while further reducing microbial diversity. Yet, how gut microbiome alterations impinge on lung adenocarcinoma development remains poorly understood. In this study, we investigated the role of gut microbiome changes in lung adenocarcinoma development using fecal microbiota transfer and delineated a pathway by which gut microbiome alterations incurred by loss of Lcn2 fostered the proliferation of proinflammatory bacteria of the genus Alistipes, triggering gut inflammation. This inflammation propagated systemically, exerting immunosuppression within the tumor microenvironment, augmenting tumor growth through an IL6-dependent mechanism and dampening response to immunotherapy. Corroborating our preclinical findings, we found that patients with lung adenocarcinoma with a higher relative abundance of Alistipes species in the gut showed diminished response to neoadjuvant immunotherapy. These insights reveal the role of microbiome-induced inflammation in lung adenocarcinoma and present new potential targets for interception and therapy.},
}
@article {pmid39621607,
year = {2024},
author = {Deel, HL and Manter, DK and Moore, JM},
title = {Rethreading the needle: A novel molecular index of soil health (MISH) using microbial functional genes to predict soil health management.},
journal = {PloS one},
volume = {19},
number = {12},
pages = {e0314072},
doi = {10.1371/journal.pone.0314072},
pmid = {39621607},
issn = {1932-6203},
mesh = {*Soil Microbiology ; *Soil/chemistry ; *RNA, Ribosomal, 16S/genetics ; Metagenome ; Bacteria/genetics/classification/isolation &amp; purification ; Microbiota/genetics ; Machine Learning ; Ecosystem ; Genes, Microbial ; },
abstract = {Soil health relies on the actions and interactions of an abundant and diverse biological community. Current soil health assessments rely heavily on a suite of soil biological, chemical, and physical indicators, often excluding molecular information. Soil health is critical for sustainable agricultural production, and a comprehensive understanding of how microbial communities provide ecosystem services can help guide management practices. To explore the role of microbial function in soil health, 536 soil samples were collected from 26 U.S. states, representing 52 different crops and grazing lands, and analyzed for various soil health indicators. The bacterial functional profile was characterized using 16S ribosomal RNA gene sequencing paired with PICRUSt2 to predict metagenome functions. Functional data were used as predictors in eXtreme Gradient Boosting (XGBoost), a powerful machine learning algorithm, and enzymes important to soil health indicators were compiled into a Molecular Index of Soil Health (MISH). The overall MISH score significantly correlated with non-molecular measures of soil health and management practice adoption. Additionally, several new enzymes were identified as potential targets to better understand microbial mediation of soil health. This low-cost, DNA-based approach to measuring soil health is robust and generalizable across climates.},
}
@article {pmid39621289,
year = {2024},
author = {Salam, LB and Apollos, EE and Obayori, OS and Michael, GI},
title = {Physicochemistry and comparative metagenomics of a tropical estuary persistently inundated with anthropogenic pollutants.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {39621289},
issn = {1874-9356},
abstract = {The physicochemistry, metabolic properties, and microbial community structure of a tropical estuary persistently inundated with anthropogenic pollutants were elucidated using diverse analytical tools and a shotgun metagenomics approach. The physicochemistry of the Awoye estuary surface water (AEW) and sediment (AES) revealed higher values in the sediment for most of the parameters analyzed, while aside from copper and zinc, the concentrations of the detected heavy metals (Cd, Cr, Pb, Fe, As, Ni, Hg, Mn, Se) in the water and sediment were higher than the acceptable thresholds. Hydrocarbon content analysis revealed increasingly high concentrations of high molecular weight polycyclic aromatic hydrocarbons (HMW PAHs) in the sediment. Structurally, the predominant taxa in the AEW metagenome are Proteobacteria (50.35%), Alphaproteobacteria (43.31%), Brevundimonas (49.96%), and Leptolyngbya boryana (14.93%), while in the sediment (AES) metagenome, Proteobacteria (53.03%), Gammaproteobacteria (28.66%), Azospirillum (6.51%), and Acidihalobacter prosperus (7.56%) were preponderant. Statistical analysis of the two microbiomes (AEW, AES) revealed significant statistical differences (P < 0.05) at all the hierarchical levels. Functional characterization of the two metagenomes revealed extensive adaptations of the sediment microbiome to various environmental stressors as evident in the high numbers of putative genes involved in the degradation of diverse classes of aromatic hydrocarbons, efflux, detoxification, and transport of heavy metals, and metabolism of organic/inorganic nutrients. Findings from this study revealed that the estuary sediment is the sink for most of the anthropogenic pollutants and harbors the more adapted microbiome that could serve as a potential bioresource for the bioremediation of the perturbed estuary.},
}
@article {pmid39621260,
year = {2025},
author = {Gigante, CM and Weigand, MR and Li, Y},
title = {Orthopoxvirus Genome Sequencing, Assembly, and Analysis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2860},
number = {},
pages = {39-63},
pmid = {39621260},
issn = {1940-6029},
mesh = {*Orthopoxvirus/genetics ; *Genome, Viral ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; Computational Biology/methods ; Metagenomics/methods ; Poxviridae Infections/virology ; Sequence Analysis, DNA/methods ; Molecular Sequence Annotation ; Whole Genome Sequencing/methods ; },
abstract = {Poxviruses have exceptionally large genomes compared to most other viruses, which represent unique challenges to sequencing and assembly due to complex features such as repeat elements and low complexity sequences. The 2022 global mpox outbreak led to an unprecedented level of poxvirus sequencing as public health and research institutions faced with large sample numbers and demand for fast turnaround, merged NGS protocols designed for small RNA viruses with poxvirus expertise. Traditional manual assembly, checking, and editing of genomes was not feasible. Here, we present a protocol for metagenomic sequencing and orthopoxvirus genome assembly directly from DNA extracted from a patient lesion swab with no viral enrichment or host depletion. This sequencing approach is cost effective when using high throughput sequencing instruments and allows for detection of genomic insertions, deletions, and large rearrangement with confidence. We describe usage of two publicly available bioinformatic pipelines for genome assembly, quality control, annotation, and submission to sequence repositories.},
}
@article {pmid39621089,
year = {2024},
author = {Singh, K and Gupta, JK and Chanchal, DK and Shinde, MG and Kumar, S and Jain, D and Almarhoon, ZM and Alshahrani, AM and Calina, D and Sharifi-Rad, J and Tripathi, A},
title = {Natural products as drug leads: exploring their potential in drug discovery and development.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {39621089},
issn = {1432-1912},
abstract = {Natural products have been pivotal in drug discovery, offering a wealth of bioactive compounds that significantly contribute to therapeutic developments. Despite the rise of synthetic chemistry, natural products continue to play a crucial role due to their unique chemical structures and diverse biological activities. This study reviews and evaluates the potential of natural products in drug discovery and development, emphasizing the integration of traditional knowledge with modern drug discovery methodologies and addressing the associated challenges. A comprehensive literature search was conducted across PubMed/MedLine, Scopus, Web of Science, Google Scholar, and Cochrane Library, covering publications from 2000 to 2023. Inclusion criteria focused on studies related to natural products, bioactive compounds, medicinal plants, phytochemistry, and AI applications in drug discovery. Data were categorized into source, extraction methods, bioactivity assays, and technological advances. The current review underscores the historical and ongoing importance of natural products in drug discovery. Technological advancements in chromatographic and spectroscopic techniques have improved the isolation and structural elucidation of bioactive compounds. AI and machine learning have streamlined the identification and optimization of natural product leads. Challenges such as biodiversity sustainability and development complexities are discussed, alongside innovative approaches like biosynthetic engineering and metagenomics. Natural products remain a vital source of novel therapeutic agents, providing unique chemical diversity and specific biological activities. Integrating traditional knowledge with modern scientific methods is essential for maximizing the potential of natural products in drug discovery. Despite existing challenges, ongoing research and technological advancements are expected to enhance the efficiency and success of natural product-based drug development.},
}
@article {pmid39620486,
year = {2024},
author = {Luo, Y and Sheikh, TMM and Li, X and Yuan, Y and Yao, F and Wang, M and Guo, X and Wu, J and Shafiq, M and Xie, Q and Jiao, X},
title = {Exploring the dynamics of gut microbiota, antibiotic resistance, and chemotherapy impact in acute leukemia patients: A comprehensive metagenomic analysis.},
journal = {Virulence},
volume = {15},
number = {1},
pages = {2428843},
doi = {10.1080/21505594.2024.2428843},
pmid = {39620486},
issn = {2150-5608},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Metagenomics ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Male ; Female ; Adult ; Middle Aged ; Feces/microbiology ; Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Leukemia/drug therapy/microbiology/complications ; Drug Resistance, Microbial/genetics ; Aged ; Young Adult ; Antineoplastic Agents/adverse effects ; },
abstract = {Leukemia poses significant challenges to its treatment, and understanding its complex pathogenesis is crucial. This study used metagenomic sequencing to investigate the interplay between chemotherapy, gut microbiota, and antibiotic resistance in patients with acute leukemia (AL). Pre- and post-chemotherapy stool samples from patients revealed alterations in microbial richness, taxa, and antibiotic resistance genes (ARGs). The analysis revealed a decreased alpha diversity, increased dispersion in post-chemotherapy samples, and changes in the abundance of specific bacteria. Key bacteria such as Enterococcus, Klebsiella, and Escherichia coli have been identified as prevalent ARG carriers. Correlation analysis between gut microbiota and blood indicators revealed potential links between microbial species and inflammatory biomarkers, including C-reactive protein (CRP) and adenosine deaminase (ADA). This study investigated the impact of antibiotic dosage on microbiota and ARGs, revealing networks connecting co-occurring ARGs with microbial species (179 nodes, 206 edges), and networks associated with ARGs and antibiotic dosages (50 nodes, 50 edges). Antibiotics such as cephamycin and sulfonamide led to multidrug-resistant Klebsiella colonization. Our analyses revealed distinct microbial profiles with Salmonella enterica elevated post-chemotherapy in NF patients and Akkermansia muciniphila elevated pre-chemotherapy. These microbial signatures could inform strategies to modulate the gut microbiome, potentially mitigating the risk of neutropenic fever in patients undergoing chemotherapy. Finally, a comprehensive analysis of KEGG modules shed light on disrupted metabolic pathways after chemotherapy, providing insights into potential targets for managing side effects. Overall, this study revealed intricate relationships between gut microbiota, chemotherapy, and antibiotic resistance, providing new insights into improving therapy and enhancing patient outcomes.},
}
@article {pmid39620359,
year = {2024},
author = {López-Agudelo, VA and Falk-Paulsen, M and Bharti, R and Rehman, A and Sommer, F and Wacker, EM and Ellinghaus, D and Luzius, A and Sievers, LK and Liebeke, M and Kaser, A and Rosenstiel, P},
title = {Defective Atg16l1 in intestinal epithelial cells links to altered fecal microbiota and metabolic shifts during pregnancy in mice.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2429267},
doi = {10.1080/19490976.2024.2429267},
pmid = {39620359},
issn = {1949-0984},
mesh = {Animals ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; Mice ; *Feces/microbiology ; *Autophagy-Related Proteins/genetics/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Intestinal Mucosa/microbiology/metabolism ; Epithelial Cells/microbiology/metabolism ; Crohn Disease/microbiology/metabolism ; Mice, Inbred C57BL ; Metagenomics ; Chemokine CXCL1/genetics/metabolism ; },
abstract = {Throughout gestation, the female body undergoes a series of transformations, including profound alterations in intestinal microbial communities. Changes gradually increase toward the end of pregnancy and comprise reduced α-diversity of microbial communities and an increased propensity for energy harvest. Despite the importance of the intestinal microbiota for the pathophysiology of inflammatory bowel diseases, very little is known about the relationship between these microbiota shifts and pregnancy-associated complications of the disease. Here, we explored the longitudinal dynamics of gut microbiota composition and functional potential during pregnancy and after lactation in Atg16l1[∆IEC] mice carrying an intestinal epithelial deletion of the Crohn's disease risk gene Atg16l1. Using 16S rRNA amplicon and shotgun metagenomic sequencing, we demonstrated divergent temporal shifts in microbial composition between Atg16l1 wildtype and Atg16l1[∆IEC] pregnant mice in trimester 3, which was validated in an independent experiment. Observed differences included microbial genera implicated in IBD such as Lachnospiraceae, Roseburia, Ruminococcus, and Turicibacter. Changes partially recovered after lactation. Additionally, metagenomic and metabolomic analyses suggest an increased capacity for chitin degradation, resulting in higher levels of free N-acetyl-glucosamine products in feces, alongside reduced glucose and myo-inositol levels in serum around the time of delivery. On the host side, we found that the immunological response of Atg16l1[∆IEC] mice is characterized by higher colonic mRNA levels of TNFα and CXCL1 in trimester 3 and a lower weight of offspring at birth. Understanding pregnancy-dependent microbiome changes in the context of IBD may constitute the first step in the identification of fecal microbial biomarkers and microbiota-directed therapies that could help improve precision care for managing pregnancies in IBD patients.},
}
@article {pmid39620249,
year = {2024},
author = {Kim, LY and Schüssler-Fiorenza Rose, SM and Mengelkoch, S and Moriarity, DP and Gassen, J and Alley, JC and Roos, LG and Jiang, T and Alavi, A and Thota, DD and Zhang, X and Perelman, D and Kodish, T and Krupnick, JL and May, M and Bowman, K and Hua, J and Liao, YJ and Lieberman, AF and Butte, AJ and Lester, P and Thyne, SM and Hilton, JF and Snyder, MP and Slavich, GM},
title = {California Stress, Trauma, and Resilience Study (CalSTARS) protocol: A multiomics-based cross-sectional investigation and randomized controlled trial to elucidate the biology of ACEs and test a precision intervention for reducing stress and enhancing resilience.},
journal = {Stress (Amsterdam, Netherlands)},
volume = {27},
number = {1},
pages = {2401788},
doi = {10.1080/10253890.2024.2401788},
pmid = {39620249},
issn = {1607-8888},
mesh = {Humans ; Cross-Sectional Studies ; *Stress, Psychological ; *Resilience, Psychological ; *Adverse Childhood Experiences ; California ; Adult ; Female ; Male ; Precision Medicine/methods ; Multiomics ; },
abstract = {Adverse Childhood Experiences (ACEs) are very common and presently implicated in 9 out of 10 leading causes of death in the United States. Despite this fact, our mechanistic understanding of how ACEs impact health is limited. Moreover, interventions for reducing stress presently use a one-size-fits-all approach that involves no treatment tailoring or precision. To address these issues, we developed a combined cross-sectional study and randomized controlled trial, called the California Stress, Trauma, and Resilience Study (CalSTARS), to (a) characterize how ACEs influence multisystem biological functioning in adults with all levels of ACE burden and current perceived stress, using multiomics and other complementary approaches, and (b) test the efficacy of our new California Precision Intervention for Stress and Resilience (PRECISE) in adults with elevated perceived stress levels who have experienced the full range of ACEs. The primary trial outcome is perceived stress, and the secondary outcomes span a variety of psychological, emotional, biological, and behavioral variables, as assessed using self-report measures, wearable technologies, and extensive biospecimens (i.e. DNA, saliva, blood, urine, &amp; stool) that will be subjected to genomic, transcriptomic, proteomic, metabolomic, lipidomic, immunomic, and metagenomic/microbiome analysis. In this protocol paper, we describe the scientific gaps motivating this study as well as the sample, study design, procedures, measures, and planned analyses. Ultimately, our goal is to leverage the power of cutting-edge tools from psychology, multiomics, precision medicine, and translational bioinformatics to identify social, molecular, and immunological processes that can be targeted to reduce stress-related disease risk and enhance biopsychosocial resilience in individuals and communities worldwide.},
}
@article {pmid39620245,
year = {2024},
author = {Fukuda, S and Akatsu, T and Fujii, A and Kawano, S and Minegishi, Y and Ota, N},
title = {Commensal Neisseria Inhibit Porphyromonas Gingivalis Invasion of Gingival Epithelial Cells.},
journal = {Oral health &amp; preventive dentistry},
volume = {22},
number = {},
pages = {609-616},
doi = {10.3290/j.ohpd.b5866430},
pmid = {39620245},
issn = {1757-9996},
mesh = {*Porphyromonas gingivalis ; *Gingiva/microbiology ; Humans ; *Epithelial Cells/microbiology ; *Neisseria ; *Microscopy, Electron, Scanning ; Flow Cytometry ; },
abstract = {PURPOSE: Periodontal disease is caused by periodontal invasion by pathogens such as Porphyromonas gingivalis. Although recent metagenomic analyses have shown that oral commensal bacteria are abundant in the mouth of healthy individuals, few studies have experimentally verified the benefits and functions of oral commensal bacteria in periodontal diseases. In this study, we focused on Neisseria among the oral commensal bacteria and aimed to experimentally verify its effects on P. gingivalis invasion.<br><br>MATERIALS AND METHODS: We evaluated the inhibitory effect of Neisseria spp. on P. gingivalis invasion using a flow cytometry-based invasion assay and analysed bacterial interactions by visualisation using scanning electron microscopy. Furthermore, we constructed a new experimental pre-mixed culture system that reproduced the interaction environment to evaluate the relevance of this interaction in invasion inhibition.<br><br>RESULTS: Flow cytometry-based invasion assays showed that all Neisseria spp. inhibited P. gingivalis invasion, with Neisseria mucosa and Neisseria elongata being particularly effective. Interaction analysis using scanning electron microscopy showed that N. mucosa and N. elongata, which have strong inhibitory effects on P. gingivalis invasion, interacted with P. gingivalis at high frequencies.<br><br>CONCLUSION: Commensal Neisseria was found to exert a beneficial function by directly interacting with P. gingivalis and inhibiting its invasion of gingival epithelial cells. These results suggest that Neisseria, as a probiotic or synbiotic oral commensal, may represent an innovative approach to preventing periodontal disease.},
}
@article {pmid39620111,
year = {2024},
author = {Zhao, J and Wang, C and Hu, J and Ma, R and Yu, B and Zhao, W and Wang, H and Gu, Y and Zhang, J},
title = {Corrigendum: Integrated metagenomics and metabolomics analyses revealed biomarkers in β-casein A2A2-type cows.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1518338},
doi = {10.3389/fvets.2024.1518338},
pmid = {39620111},
issn = {2297-1769},
abstract = {[This corrects the article DOI: 10.3389/fvets.2024.1438717.].},
}
@article {pmid39620093,
year = {2024},
author = {Thompson, CC and Wasielesky, W and Landuci, F and Lima, MS and Bacha, L and Perazzolo, LM and Lourenço-Marques, C and Soares, F and Pousão-Ferreira, P and Hanson, L and Gomez-Gil, B and Thompson, M and Varasteh, T and Silva, TA and Swings, J and Zhang, XH and de Souza, W and Thompson, FL},
title = {Understanding the role of microbes in health and disease of farmed aquatic organisms.},
journal = {Marine life science &amp; technology},
volume = {6},
number = {4},
pages = {579-609},
pmid = {39620093},
issn = {2662-1746},
abstract = {Aquaculture is critical to reduce protein deficiencies and supplement the world's demand for seafood. However, the culture environment predisposes farmed animals to infectious diseases. In particular, the high density of fish, crustacean, mollusk, sea cucumber or algal species allows for the rapid spread of infectious diseases resulting in devastating losses. Massive amounts of antibiotics have been used to sustain aquaculture production. This has led to the critical need to evaluate the impact of current control measures and optimize disease management schemes with an emphasis on global impact and sustainability. Furthermore, local and global changes have enhanced the pathogens' effects over aquaculture settings because increased temperature and pollution may trigger virulence genes and toxin production. Technological developments including biofloc technology, integrated multitrophic systems, recirculating aquaculture systems and probiotics have contributed to enhancing aquaculture sustainability and reducing the need for high loads of antibiotics and other chemicals. Furthermore, biotechnological tools (e.g., omics and cell biology) have shed light on cellular processes in the health and disease of reared organisms. Metagenomics is a reliable and relatively quick tool to identify microbial communities in aquaculture settings.},
}
@article {pmid39619951,
year = {2024},
author = {Wang, X and Hu, X and He, W and Yin, JY},
title = {Inulin does not affect trimethylamine N-oxide formation in mice with a high-fat diet combined with choline and L-carnitine.},
journal = {Food science &amp; nutrition},
volume = {12},
number = {11},
pages = {8968-8977},
pmid = {39619951},
issn = {2048-7177},
abstract = {Emerging evidence suggests that gut bacteria-derived trimethylamine N-oxide (TMAO) elevates the risk of cardiovascular disease, and dietary fiber holds the potential to attenuate TMAO formation. However, the effectiveness of dietary fiber, such as inulin, in inhibiting TMAO formation remains controversial. Therefore, this study investigated the effect of inulin supplementation on TMAO formation in mice with high TMAO levels induced by a high-fat diet (HFD) combined with choline and L-carnitine. Results showed that HFD treatment significantly elevated blood TMAO concentrations and increased the abundances of TMAO formation-associated gut bacteria, as well as the abundances of functional genes responsible for TMA formation. While the supplementation of choline and L-carnitine greatly enhanced blood trimethylamine (TMA) and TMAO levels, inulin supplementation did not significantly affect TMAO levels and had limited impact on TMA-associated gut bacteria, except for Desulfitobacterium hafniense.},
}
@article {pmid39619731,
year = {2024},
author = {Wen, S and Zeng, JJ and Li, Y},
title = {Rickettsia felis Pulmonary Infection Detected via Metagenomic Next-Generation Sequencing in a Clonorchiasis Patient: A Case Report.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {5189-5194},
pmid = {39619731},
issn = {1178-6973},
abstract = {Rickettsia felis (R. felis) is a Gram-negative obligate intracellular bacterium with a global presence across various hosts, including mammals, humans, and ectoparasites. Herein, we present a case of R. felis infection in a previously healthy 43-year-old male with a history of Clonorchis sinensis and recent corticosteroid use. The identification of R. felis was accomplished through metagenomic next-generation sequencing (mNGS) of the patient's bronchoalveolar lavage fluid (BALF). This case represents the first documented pulmonary infection caused by R. felis in China, confirmed by mNGS analysis of bronchoalveolar lavage fluid (BALF) and reported from Shenzhen, China.},
}
@article {pmid39619691,
year = {2024},
author = {Xie, R and Danso, B and Sun, J and Al-Tohamy, R and Khalil, MA and Schagerl, M and Ali, SS},
title = {Metagenomics analysis of bacterial community structure from wood- and soil-feeding termites: metabolic pathways and functional structures toward the degradation of lignocellulose and recalcitrant compounds.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1424982},
pmid = {39619691},
issn = {1664-302X},
abstract = {Some essential information on gut bacterial profiles and their unique contributions to food digestion in wood-feeding termites (WFT) and soil-feeding termites (SFT) is still inadequate. The feeding type of termites is hypothesized to influence their gut bacterial composition and its functionality in degrading lignocellulose or other organic chemicals. This could potentially provide alternative approaches for the degradation of some recalcitrant environmental chemicals. Therefore, metagenomic analysis can be employed to examine the composition and functional profiles of gut bacterial symbionts in WFT and SFT. Based on the metagenomic analysis of the 16S rRNA gene sequences of gut bacterial symbionts in the WFT, Microcerotermes sp., and the SFT, Pericapritermes nitobei, the findings revealed a total of 26 major bacterial phyla, with 18 phyla commonly represented in both termites, albeit in varying abundances. Spirochaetes dominated the bacterial symbionts in Microcerotermes sp. at 55%, followed by Fibrobacters, while Firmicutes dominated the gut bacteria symbionts in P. nitobei at 95%, with Actinobacteria coming in second at 2%. Furthermore, the Shannon and phylogenetic tree diversity indices, as well as the observed operational taxonomic units and Chao 1 richness indices, were all found to be higher in the WFT than in the SFT deduced from the alpha diversity analysis. Based on the principal coordinate analysis, exhibited a significant distance dissimilarity between the gut bacterial symbionts. The results showed that the gut bacterial composition differed significantly between the WFT and SFT. Furthermore, Tax4Fun analysis evaluated bacterial functions, revealing the predominance of carbohydrate metabolism, followed by amino acid metabolism and energy metabolism in both Microcerotermes sp. and P. nitobei termites. The results implicated that bacterial symbionts inhabiting the guts of both termites were actively involved in the degradation of lignocellulose and other recalcitrant compounds.},
}
@article {pmid39619690,
year = {2024},
author = {Wu, X and Liu, X and Xu, W and Chen, W and Zhong, Z and Tan, H and Xiang, T},
title = {A nested case-control study on the association of gut virome in early pregnancy and gestational diabetes mellitus.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1461259},
pmid = {39619690},
issn = {1664-302X},
abstract = {BACKGROUND: Recent studies have increasingly shown the connection between gut microbiome and gestational diabetes mellitus (GDM). However, no studies have explored the relationship between the gut virome and GDM, and the underlying mechanism remains unknown.<br><br>METHODS: We performed a nested case-control study within a follow-up cohort, enrolling 51 patients with GDM and 51 healthy controls. Shotgun metagenomics sequencing was used to explore gut virome profiles during early pregnancy.<br><br>RESULTS: Diversity analysis revealed no difference in the overall gut virome composition between two groups, however, we found greater abundance of Escherichia phage SH2026Stx1 (Q = 0.23), Enterobacteria phage mEp043 c-1 (Q = 0.21), crAssphage cr50_1 (Q = 0.21), Enterobacteria phage phi80 (Q = 0.21), and Escherichia phage HK106 (Q = 0.23) in GDM patients. Cross-kingdom correlation analysis showed the negative correlation between the gut bacterium Eubacterium eligens and three bacteriophages (Escherichia phage SH2026Stx1, Enterobacteria phage mEp043 c-1, and Escherichia phage HK106) in GDM group (r < 0, P < 0.05). Based on gut microbial features and clinical indicators, we constructed a new prediction model using random forest method for GDM with good predictive performance (AUC of 0.893, 95% CI: 0.736 &#x223c; 0.990).<br><br>CONCLUSION: This study is the first to investigate the relationship between the gut virome and GDM as well as the cross-kingdom correlation between gut viruses and bacteria in GDM. Our findings could enhance strategies for preventing and treating GDM from the perspective of gut microbiome, offering valuable insights into its pathogenesis.},
}
@article {pmid39619689,
year = {2024},
author = {Wang, C and Wang, D and Li, C and Ge, Z and Hao, L and Albasher, G and Feng, F and Sun, Y and Lyu, Y and Zheng, S},
title = {Microbial communities during the composting process of Agaricus subrufescens and their effects on mushroom agronomic and nutritional qualities.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1471638},
pmid = {39619689},
issn = {1664-302X},
abstract = {INTRODUCTION: Tunnel composting technology for preparing Agaricus subrufescens cultivation media can achieve a higher biological efficiency (BE) and a lower contamination rate (CR). However, this technology lacks in-depth and systematic study.<br><br>METHODS: In the present study, the changes in the microbiome and microbial metabolic functions were surveyed using metagenomic analysis. The physicochemical parameters, agronomic properties and nutritional qualities were also evaluated.<br><br>RESULTS AND DISCUSSION: Results showed that the contents of cellulose, hemicellulose and lignin dropped to 10.18, 11.58, 27.53%, respectively at the end of composting. The tunnel composting technology led to significant increases in crude protein content (32.56%) and crude fiber content (13.68%). Variations of physicochemical characteristics led to different successions of microbial communities. Bacteria manifested significantly higher abundance than fungi. Firmicutes, Actinobacteriota, Chloroffexi and Deinococcota were the predominant bacterial phyla. Ascomycota and Basidiomycota were the dominant fungal phyla in the thermophilic phase. Pseudonocardia, Truepera, and Thermopolyspora were positively correlated with the yield of A. subrufescens. In addition to TN, most of the physicochemical properties were significantly correlated with fungal communities in the thermophilic phase. The metabolisms of carbohydrate, amino acid and energy were the primary enrichment pathways. These findings deepen the understanding of microbial communities composition during the composting of A. subrufescens substrates. Moreover, this study provides a basis for improving tunnel composting technology.},
}
@article {pmid39619659,
year = {2024},
author = {Zhao, Y and Zhang, W and Zhang, X},
title = {Application of metagenomic next-generation sequencing in the diagnosis of infectious diseases.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1458316},
pmid = {39619659},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Communicable Diseases/diagnosis/microbiology ; Molecular Diagnostic Techniques/methods ; Bacteria/genetics/isolation &amp; purification/classification ; Viruses/genetics/isolation &amp; purification/classification ; },
abstract = {Metagenomic next-generation sequencing (mNGS) is a transformative approach in the diagnosis of infectious diseases, utilizing unbiased high-throughput sequencing to directly detect and characterize microbial genomes from clinical samples. This review comprehensively outlines the fundamental principles, sequencing workflow, and platforms utilized in mNGS technology. The methodological backbone involves shotgun sequencing of total nucleic acids extracted from diverse sample types, enabling simultaneous detection of bacteria, viruses, fungi, and parasites without prior knowledge of the infectious agent. Key advantages of mNGS include its capability to identify rare, novel, or unculturable pathogens, providing a more comprehensive view of microbial communities compared to traditional culture-based methods. Despite these strengths, challenges such as data analysis complexity, high cost, and the need for optimized sample preparation protocols remain significant hurdles. The application of mNGS across various systemic infections highlights its clinical utility. Case studies discussed in this review illustrate its efficacy in diagnosing respiratory tract infections, bloodstream infections, central nervous system infections, gastrointestinal infections, and others. By rapidly identifying pathogens and their genomic characteristics, mNGS facilitates timely and targeted therapeutic interventions, thereby improving patient outcomes and infection control measures. Looking ahead, the future of mNGS in infectious disease diagnostics appears promising. Advances in bioinformatics tools and sequencing technologies are anticipated to streamline data analysis, enhance sensitivity and specificity, and reduce turnaround times. Integration with clinical decision support systems promises to further optimize mNGS utilization in routine clinical practice. In conclusion, mNGS represents a paradigm shift in the field of infectious disease diagnostics, offering unparalleled insights into microbial diversity and pathogenesis. While challenges persist, ongoing technological advancements hold immense potential to consolidate mNGS as a pivotal tool in the armamentarium of modern medicine, empowering clinicians with precise, rapid, and comprehensive pathogen detection capabilities.},
}
@article {pmid39619641,
year = {2024},
author = {Xia, T and Huang, F and Yun, F and Liu, Y and Wang, T and Wang, S and Jin, S and Ma, X and Wang, W and He, J and Teng, K and Zhong, J},
title = {Lacticaseibacillus rhamnosus LRJ-1 alleviates constipation through promoting gut Bacteroides-derived γ-aminobutyric acid production.},
journal = {Current research in food science},
volume = {9},
number = {},
pages = {100924},
pmid = {39619641},
issn = {2665-9271},
abstract = {Multiple gastrointestinal disorders are associated with impaired gut microbiota. Probiotic Lacticaseibacillus rhamnosus can improve bowel disorder, however, the action mechanism is poorly understood. We integrated multi-omics data from the gut metagenome, metabolome, and colon transcriptome of constipated mice underlying L. rhamnosus LRJ-1 treatment to provide insights into host-microbial metabolic pathway. We found that oral administration of L. rhamnosus LRJ-1 alleviated constipation in mice accompanied by the increased abundances of fecal γ-aminobutyric acid (GABA) and intestinal commensal Bacteroides, and the activation of host GABAergic synapses. B. uniformis was the most enriched Bacteroides species in constipated mice treated with L. rhamnosus LRJ-1, and contributed to the increased abundance of GABA in the gut. Administration of either B. uniformis ATCC 8492 or GABA alleviated constipation and increased gastrointestinal motility in constipated mice. Knockout of the GABA biosynthetic gad gene in B. uniformis ATCC 8492 decreased GABA production and blocked its beneficial effects on constipation. These results confirm the therapeutic potential of L. rhamnosus LRJ-1 in alleviating constipation through promoting gut commensal Bacteroides-derived GABA production. Targeting the gut microbiome to regulate GABA production may open new insights for efficient constipation treatment.},
}
@article {pmid39619416,
year = {2024},
author = {Petrone, ME and Charon, J and Grigg, MJ and William, T and Rajahram, GS and Westaway, J and Piera, KA and Shi, M and Anstey, NM and Holmes, EC},
title = {A virus associated with the zoonotic pathogen Plasmodium knowlesi causing human malaria is a member of a diverse and unclassified viral taxon.},
journal = {Virus evolution},
volume = {10},
number = {1},
pages = {veae091},
pmid = {39619416},
issn = {2057-1577},
abstract = {The Apicomplexa are a phylum of single-celled eukaryotes that can infect humans and include the mosquito-borne parasite Plasmodium, the cause of malaria. Viruses that infect non-Plasmodium spp. disease-causing protozoa affect the pathogen life cycle and disease outcomes. However, only one RNA virus (Matryoshka RNA virus 1) has been identified in Plasmodium, and none have been identified in zoonotic Plasmodium species. The rapid expansion of the known RNA virosphere via metagenomic sequencing suggests that this dearth is due to the divergent nature of RNA viruses that infect protozoa. We leveraged newly uncovered data sets to explore the virome of human-infecting Plasmodium species collected in Sabah, east (Borneo) Malaysia. From this, we identified a highly divergent RNA virus in two human-infecting P. knowlesi isolates that is related to the unclassified group 'ormycoviruses'. By characterizing 15 additional ormycoviruses identified in the transcriptomes of arthropods, we show that this group of viruses exhibits a complex ecology as noninfecting passengers at the arthropod-mammal interface. With the addition of viral diversity discovered using the artificial intelligence-based analysis of metagenomic data, we also demonstrate that the ormycoviruses are part of a diverse and unclassified viral taxon. This is the first observation of an RNA virus in a zoonotic Plasmodium species. By linking small-scale experimental data to advances in large-scale virus discovery, we characterize the diversity and confirm the putative genomic architecture of an unclassified viral taxon. This approach can be used to further explore the virome of disease-causing Apicomplexa and better understand how protozoa-infecting viruses may affect parasite fitness, pathobiology, and treatment outcomes.},
}
@article {pmid39619205,
year = {2024},
author = {Hewson, I and Brandt, M and Budd, K and Breitbart, M and DeRito, C and Gittens, S and Henson, MW and Hylkema, A and Sevier, M and Souza, M and Vilanova-Cuevas, B and Von Hoene, S},
title = {Viral metagenomic investigation of two Caribbean echinoderms, Diadema antillarum (Echinoidea) and Holothuria floridana (Holothuria).},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e18321},
pmid = {39619205},
issn = {2167-8359},
mesh = {Animals ; *Metagenomics ; Caribbean Region ; *Genome, Viral/genetics ; Echinodermata/virology ; Metagenome ; Holothuria/virology/genetics ; Coral Reefs ; Viruses/genetics/isolation &amp; purification/classification ; Virome/genetics ; },
abstract = {BACKGROUND: Echinoderms play crucial roles in coral reef ecosystems, where they are significant detritivores and herbivores. The phylum is widely known for its boom and bust cycles, driven by food availability, predation pressure and mass mortalities. Hence, surveillance of potential pathogens and associates of grossly normal specimens is important to understanding their roles in ecology and mass mortality.<br><br>METHODS: We performed viral surveillance in two common coral reef echinoderms, Diadema antillarum and Holothuria floridana, using metagenomics. Urchin specimens were obtained during the 2022 Diadema antillarum scuticociliatosis mass mortality event from the Caribbean and grossly normal H. floridana specimens from a reef in Florida. Viral metagenomes were assembled and aligned against viral genomes and protein encoding regions. Metagenomic reads and previously sequenced transcriptomes were further investigated for putative viral elements by Kraken2.<br><br>RESULTS: D. antillarum was devoid of viruses typically seen in echinoderms, but H. floridana yielded viral taxa similar to those found in other sea cucumbers, including Pisoniviricetes (Picornaviruses), Ellioviricetes (Bunyaviruses), and Magsaviricetes (Nodaviruses). The lack of viruses detected in D. antillarum may be due to the large amount of host DNA in viral metagenomes, or because viruses are less abundant in D. antillarum tissues when compared to H. floridana tissues. Our results also suggest that RNA amplification approach may influence viral representation in viral metagenomes. While our survey was successful in describing viruses associated with both echinoderms, our results indicate that viruses are less pronounced in D. antillarum than in other echinoderms. These results are important in context of wider investigation on the association between viruses and D. antillarum mass mortalities, since the conventional method used in this study was unsuccessful.},
}
@article {pmid39618850,
year = {2024},
author = {Liu, H and Feng, S and Tang, M and Tian, R and Zhang, S},
title = {Gut Commensal Bacteroides thetaiotaomicron Promote Atherothrombosis via Regulating L-Tryptophan Metabolism.},
journal = {Reviews in cardiovascular medicine},
volume = {25},
number = {11},
pages = {395},
pmid = {39618850},
issn = {2153-8174},
abstract = {BACKGROUND: Coronary thrombosis events continue to be the leading cause of morbidity and mortality worldwide. Recently, emerging evidence has highlighted the role of gut microbiota in cardiovascular disease, but few studies have systematically investigated the gut microbiota variation associated with atherothrombosis.<br><br>METHODS: We conducted multi-omics analysis (metagenomics sequencing and serum metabolomics) on 146 subjects from Peking Union Medical College Hospital-Coronary Artery Disease (PUMCH-CAD) cohort. We analyzed the key strains and metabolic pathways related to coronary artery disease (CAD) development, explored the bacterial functional pathway which contributes to atherothrombosis at strain level in depth. Single strain colonization procedures on germ free mice demonstrated the promotion of platelet activation and thrombotic phenotypes of the disordered gut microbiota.<br><br>RESULTS: Gut microbiome and serum metabolome shifts were apparent in cases of CAD progression, Bacteroides spp. disturbed the development of CAD by participating in lipopolysaccharide (LPS), menaquinone and methanogenesis pathways. Particularly, coronary thrombosis is characterized by increased circulatory levels of L-tryptophan, which correlate with Bacteroides thetaiotaomicron that has enriched biosynthetic potential. In germ free mice we demonstrate that Bacteroides thetaiotaomicron colonization could induce thrombosis, aggravate platelet hyperreactivity and augment fecal levels of L-tryptophan.<br><br>CONCLUSIONS: The disordered gut microbiota of CAD contributed to the occurrence and development of atherothrombosis. The key members of the bacterial and metabolic features may become biomarkers for predicting the cardiovascular thrombosis event. Targeting the microbial pathway may have the potential to reduce the incidence of cardiovascular disorders.<br><br>CLINICAL TRIAL REGISTRATION: ChiCTR2000033897, https://www.chictr.org.cn/showproj.html?proj=55023.},
}
@article {pmid39618230,
year = {2024},
author = {Li, H and Mao, X and Wu, Z and Yu, W},
title = {Omadacycline in the Treatment of Chlamydia psittaci Pneumonia: A Retrospective Study on Efficacy and Safety.},
journal = {British journal of hospital medicine (London, England : 2005)},
volume = {85},
number = {11},
pages = {1-12},
doi = {10.12968/hmed.2024.0381},
pmid = {39618230},
issn = {1750-8460},
mesh = {Humans ; Retrospective Studies ; Male ; Female ; *Anti-Bacterial Agents/therapeutic use/adverse effects ; Middle Aged ; *Chlamydophila psittaci/isolation &amp; purification ; *Tetracyclines/therapeutic use/adverse effects ; Adult ; *Psittacosis/drug therapy/diagnosis/microbiology ; Treatment Outcome ; Aged ; C-Reactive Protein/analysis ; },
abstract = {Aims/Background Chlamydia psittaci is an obligate intracellular bacterium that primarily infects birds, but can cause respiratory infections in humans. Clinical evidence supporting the use of omadacycline for the treatment of Chlamydia psittaci pneumonia remains limited; therefore, this study aimed to evaluate the potential of omadacycline in treating Chlamydia psittaci pneumonia by analyzing the patients' clinical outcomes and the drug safety profile. Methods We retrospectively reviewed the medical records of 15 patients with Chlamydia psittaci pneumonia treated at the First Affiliated Hospital, Zhejiang University School of Medicine between January and December 2023. Following diagnosis with the aid of metagenomic next-generation sequencing, the patients received omadacycline for treatment, and their clinical outcomes and laboratory marker profiles were monitored to assess the treatment efficacy and safety. Results Significant improvements were observed in clinical symptoms and laboratory markers, including C-reactive protein (p < 0.001), procalcitonin (p = 0.001), neutrophil percentage (p < 0.001), and the SpO2/FiO2 ratio (p < 0.001), after treatment with omadacycline. A 100% cure rate was reported within 28 days of treatment initiation, with gastrointestinal disturbances being the most common side effect. Conclusion Omadacycline shows promise in treating Chlamydia psittaci pneumonia and is well tolerated by the users. However, further controlled trials involving larger samples are required to confirm the efficacy and safety of the drug.},
}
@article {pmid39616917,
year = {2024},
author = {Nassereddine, ZN and Opara, SD and Coutinho, OA and Qyteti, F and Book, R and Heinicke, MP and Napieralski, J and Tiquia-Arashiro, SM},
title = {Critical perspectives on advancing antibiotic resistant gene (ARG) detection technologies in aquatic ecosystems.},
journal = {The Science of the total environment},
volume = {957},
number = {},
pages = {177775},
doi = {10.1016/j.scitotenv.2024.177775},
pmid = {39616917},
issn = {1879-1026},
abstract = {The spread of antibiotic resistance genes (ARGs) in aquatic ecosystems poses a serious risk to environmental and public health, making advanced detection and monitoring methods essential. This review provides a fresh perspective and a critical evaluation of recent advances in detecting and monitoring ARGs in aquatic environments. It highlights the latest innovations in molecular, bioinformatic, and environmental techniques. While traditional methods like culture-based assays and polymerase chain reaction (PCR) remain important, they are increasingly being supplemented by high-throughput sequencing technologies applied to metagenomics. These technologies offer comprehensive insights into the diversity and distribution of ARGs in aquatic environments. The integration of bioinformatic tools and databases has improved the accuracy and efficiency of ARG detection, enabling the analysis of complex datasets and tracking the evolution of ARGs in aquatic settings. Additionally, new environmental monitoring methods, including novel biosensors, geographic information systems (GIS) applications, and remote sensing technologies, have emerged as powerful tools for real-time ARG surveillance in water systems. This review critically examines the challenges of standardizing these methodologies and emphasizes the need for interdisciplinary approaches to enhance ARG monitoring across different aquatic ecosystems. By assessing the strengths and limitations of various methods, this review aims to guide future research and the development of more effective strategies for managing antibiotic resistance in aquatic environments.},
}
@article {pmid39616811,
year = {2024},
author = {Riveros, A and Asefaw, BK and Wang, Q and Maqbool, T and Tang, Y and Jiang, D},
title = {Selenium treatment via integrating flow electrode capacitive deionization (FCDI) and bio-electrochemical systems (BES).},
journal = {Water research},
volume = {271},
number = {},
pages = {122844},
doi = {10.1016/j.watres.2024.122844},
pmid = {39616811},
issn = {1879-2448},
abstract = {Selenium pollution in aquatic environments poses a major global challenge, with a significant gap in effective treatment technologies. In this study, we explored a novel approach integrating flow-electrode capacitive deionization (FCDI) with bio-electrochemical systems (BES) for the removal and reduction of selenate and selenite ions in one compact reactor. Our integrated system was electricity-driven, eliminating chemical usage. Up to 76 % selenium removal from the waste streams was achieved, followed by up to 66 % and 54 % reduction of selenate and selenite to elemental selenium respectively. The addition of acetate, a carbon source, enhanced selenate reduction by 14 % but lowered selenite reduction by 21 %, suggesting the substrate-dependent and bio-electrochemical-driven nature of selenate and selenite reduction respectively. Metagenomic sequencing revealed that Geobacter sulfurreducens and Pseudomonas stutzeri two known Se-reducing species, likely contributed to both selenite and selenate reduction through up-regulating functional genes related to sulfide reductase, fumarate reductase, and multi-heme c-type cytochromes. Thauera spp. and Alishewanella spp., two species not previously associated with selenium reduction, were likely involved in selenite reduction via the up-regulation of genes related to sulfite reductase and selenium reductase.},
}
@article {pmid39616810,
year = {2024},
author = {Yen, JH and Yeh, JF and Chan, CY and Tung, HH and Chi, KH and Chen, HC and Chen, WR and Chou, CC and Hsiao, TC},
title = {Unveiling the role of aeration tanks in the emission and enrichment of airborne antibiotic resistance genes in a wastewater treatment plant.},
journal = {Water research},
volume = {271},
number = {},
pages = {122866},
doi = {10.1016/j.watres.2024.122866},
pmid = {39616810},
issn = {1879-2448},
abstract = {The aeration tanks in wastewater treatment plants (WWTPs) are important sources of airborne antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) due to bubble bursts at the air-liquid interface. This study employed an integrated metagenomic workflow, encompassing reference-based, assembly-based, and binning-based modules, to investigate resistomes in a WWTP in northern Taiwan. The role of aeration tanks in emitting airborne ARGs and their associated risks was assessed. The findings revealed a strong similarity between the ARG profiles in aeration tank wastewater and surrounding PM2.5, indicating atmospheric transmission of ARGs. Notably, the ARG level in PM2.5 (0.83 ± 0.11 ARGs/cell) was 59.6 % higher than in wastewater (0.52 ± 0.01 ARGs/cell). The assembly-based analysis showed that foam-forming bacteria such as Mycobacterium and Gordonia dominated ARGs-carrying contigs in PM2.5, suggesting that higher atomization capabilities of ARB contribute to airborne ARG prevalence. Furthermore, a significant proportion of stress response genes and increasing efflux pump resistance (122.6 %) in PM2.5 imply that mechanical forces during aerosolization and harsh atmospheric conditions select for airborne ARB capable of overcoming stress induced by dramatic environmental changes. Overall, the study indicates that ARG risk is intensified in PM2.5 due to their abundance, mobility, and pathogenicity. In conclusion, aeration tanks not only emit airborne ARGs but also cause an unexpected enrichment effect and exposure risk during aeration, highlighting the critical water-to-air transmission route of ARGs in WWTPs.},
}
@article {pmid39616689,
year = {2024},
author = {Naruse, H and Watanabe, N and Ohta, A and Shimizu, Y and Fukushima, T and Watanabe, A and Nakao, T and Taji, Y and Matsumoto, Y and Nakamura, S and Igarashi, Y and Takaki, A and Mitarai, S and Mitsutake, K and Tanaka, R and Ebihara, Y},
title = {Catheter-related bloodstream infection by a newly proposed "Mycobacterium toneyamachuris" in a boy with B-cell precursor acute lymphoblastic leukemia.},
journal = {Diagnostic microbiology and infectious disease},
volume = {111},
number = {3},
pages = {116626},
doi = {10.1016/j.diagmicrobio.2024.116626},
pmid = {39616689},
issn = {1879-0070},
abstract = {This report describes a 6-year-old boy who developed non-tuberculosis mycobacteria (NTM) catheter-related bloodstream infection (CRBSI) during treatment for B-cell precursor acute lymphoblastic leukemia. A Hickman catheter was inserted before starting treatment. He developed a fever during chemotherapy, and blood culture was drawn from the catheter. Blurred Gram-positive bacilli were found in Gram stain, looked positive in Ziehl-Neelsen stain, and were identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry as Mycobacterium mucogenicum phocaicum group. The administration of clarithromycin and amikacin was started and the Hickman catheter was removed. We performed genomic sequencing to obtain accurate identification, demonstrating that this microorganism was identified as "M. toneyamachuris" calculated by the average nucleotide identity index. Finally, a clinical diagnosis of CRBSI caused by "M. toneyamachuris" was made. Our findings suggest that genomic sequencing is available for the accurate identification of NTM species.},
}
@article {pmid39616474,
year = {2024},
author = {He, WW and Wang, WJ and Huang, ZX and Li, YL and Xia, QY and Shi, Y and Yang, B and Sun, HM},
title = {Mycobacterium paragordonae pulmonary disease with rapidly growing solitary lesions: a case report and literature review.},
journal = {Journal of infection in developing countries},
volume = {18},
number = {10},
pages = {1625-1631},
doi = {10.3855/jidc.18664},
pmid = {39616474},
issn = {1972-2680},
mesh = {Humans ; Female ; Aged ; *Mycobacterium Infections, Nontuberculous/diagnosis/microbiology/drug therapy/pathology ; *Tomography, X-Ray Computed ; Lung/pathology/microbiology/diagnostic imaging ; Nontuberculous Mycobacteria/isolation &amp; purification/genetics ; Lung Diseases/microbiology/pathology/diagnosis/drug therapy ; Anti-Bacterial Agents/therapeutic use ; High-Throughput Nucleotide Sequencing ; },
abstract = {INTRODUCTION: Mycobacterium paragordonae (MPG) is a novel and uncommon nontuberculous mycobacterium (NTM). We describe a case of MPG pulmonary disease (MPGPD) with a single, rapidly growing, pulmonary mass, which has rarely been reported.<br><br>CASE REPORT: A chest CT scan of a 66-year-old woman revealed a rapidly growing solitary mass-like lesion in the upper lobe of the right lung, which was not seen in the previous chest CT scan six months ago. H&amp;E-stained section of the CT-guided percutaneous lung tissue biopsy specimen showed chronic inflammatory changes with epithelioid granulomas. Metagenomic next-generation sequencing (mNGS) of lung tissue biopsy specimen identified MPG with a sequence number of 1617 and a confidence level of 99%. Because the subsequent MPG droplet digital PCR (MPG-ddPCR) test of the lung tissue biopsy was positive, she was eventually diagnosed with MPGPD. She was administered a quadruple oral regimen comprising clarithromycin, levofloxacin, rifampicin, and ethambutol according to the ATS/IDSA protocol for Mycobacterium gordonae (MG) infection. The chest CT scans showed a significant reduction in the lesion one month after the treatment and almost complete resolution four months later.<br><br>CONCLUSIONS: MPGPD is a rare NTM infection. The imaging manifestations of MPGPD are diverse and may even show rapid development. mNGS of tissue biopsy can enable prompt diagnosis of MPG infection and is a good alternative to routine NTM microbial testing. The ATS/IDSA protocol for MG infection is an effective treatment for MPG infection.},
}
@article {pmid39616387,
year = {2024},
author = {Huang, G and Peng, X},
title = {Genus Bithynia: morphological classification to molecular identification.},
journal = {Parasites &amp; vectors},
volume = {17},
number = {1},
pages = {496},
pmid = {39616387},
issn = {1756-3305},
support = {82060376//National Natural Science Foundation of China/ ; No.2024GXNSFAA010039//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; },
mesh = {Animals ; *Snails/parasitology ; Trematode Infections/parasitology/veterinary ; Phylogeny ; Humans ; },
abstract = {Snails of the genus Bithynia, whose primary habitat is slow-flowing ponds and ditches, serve as the first intermediate hosts of liver fluke. Currently, approximately 200 million individuals worldwide are at risk of liver fluke infection, yet questions still persist regarding the taxonomic identification of Bithynia genus, a crucial player in the transmission of this disease. Accurate taxonomic classification of the Bithynia genus could significantly enhance current understanding of the disease's transmission mechanisms. In this article we comprehensively review the extensive research conducted on Bithynia genus, spanning past inquiries up to the latest findings. The primary emphasis is placed on exploring the taxonomic identification of this genus within various technological settings. We then present a consolidated analysis of the morphological taxonomic identification methods, highlighting their strengths and limitations. We also introduce a novel perspective on the future direction of identification and classification efforts for the members of this genus, emphasizing the crucial role Bithynia plays in the epidemiological cycle of liver fluke transmission. We conclude by urging researchers to prioritize the significance of the members of this genus in the epidemiological cycle of liver fluke transmission and in control measures for disease dissemination, within the context of the vector organisms.},
}
@article {pmid39616358,
year = {2024},
author = {Dell'Olio, A and Scott, WT and Taroncher-Ferrer, S and San Onofre, N and Soriano, JM and Rubert, J},
title = {Tailored impact of dietary fibers on gut microbiota: a multi-omics comparison on the lean and obese microbial communities.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {250},
pmid = {39616358},
issn = {2049-2618},
support = {79441//'European Union's Horizon 2020 Research and Innovation programme' for the Marie Sk&#x142;odowska-Curie/ ; RYC2018-024850-I//Spanish Ministry of Science and Innovation for the Ram&#xf3;n y Cajal fellowship/ ; },
mesh = {*Dietary Fiber/metabolism ; *Obesity/microbiology ; *Gastrointestinal Microbiome ; *Malus/microbiology ; Humans ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Metagenomics ; Pectins/metabolism ; Metabolomics ; Cellulose/metabolism ; Bioreactors/microbiology ; Multiomics ; },
abstract = {BACKGROUND: Previous studies have shown that microbial communities differ in obese and lean individuals, and dietary fiber can help reduce obesity-related conditions through diet-gut microbiota interactions. However, the mechanisms by which dietary fibers shape the gut microbiota still need to be elucidated. In this in vitro study, we examined how apple fibers affect lean and obese microbial communities on a global scale. We employed a high-throughput micro-matrix bioreactor system and a multi-omics approach to identify the key microorganisms and metabolites involved in this process.<br><br>RESULTS: Initially, metagenomics and metabolomics data indicated that obese and lean microbial communities had distinct starting microbial communities. We found that obese microbial community had different characteristics, including higher levels of Ruminococcus bromii and lower levels of Faecalibacterium prausnitzii, along with an increased Firmicutes:Bacteroides ratio. Afterward, we exposed obese and lean microbial communities to an apple as a representative complex food matrix, apple pectin as a soluble fiber, and cellulose as an insoluble fiber. Dietary fibers, particularly apple pectin, reduced Acidaminococcus intestini and boosted Megasphaera and Akkermansia in the obese microbial community. Additionally, these fibers altered the production of metabolites, increasing beneficial indole microbial metabolites. Our results underscored the ability of apple and apple pectin to shape the obese gut microbiota.<br><br>CONCLUSION: We found that the obese microbial community had higher branched-chain amino acid catabolism and hexanoic acid production, potentially impacting energy balance. Apple dietary fibers, especially pectin, influenced the obese microbial community, altering both species and metabolites. Notably, the apple pectin feeding condition affected species like Klebsiella pneumoniae and Bifidobacterium longum. By using genome-scale metabolic modeling, we discovered a mutualistic cross-feeding relationship between Megasphaera sp. MJR8396C and Bifidobacterium adolescentis. This in vitro study suggests that incorporating apple fibers into the diets of obese individuals can help modify the composition of gut bacteria and improve metabolic health. This personalized approach could help mitigate the effects of obesity. Video Abstract.},
}
@article {pmid39616255,
year = {2024},
author = {Hämmerle, M and Guellil, M and Trgovec-Greif, L and Cheronet, O and Sawyer, S and Ruiz-Gartzia, I and Lizano, E and Rymbekova, A and Gelabert, P and Bernardi, P and Han, S and Rattei, T and Schuenemann, VJ and Marques-Bonet, T and Guschanski, K and Calvignac-Spencer, S and Pinhasi, R and Kuhlwilm, M},
title = {Screening great ape museum specimens for DNA viruses.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {29806},
pmid = {39616255},
issn = {2045-2322},
support = {10.47379/VRG20001//Vienna Science and Technology Fund (Wiener Wissenschafts-, Forschungs- und Technologiefonds)/ ; 864203//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 2020-03398//Vetenskaps&#xe5;det (Swedish Research Council)/ ; },
mesh = {Animals ; *Museums ; *Phylogeny ; *DNA Viruses/genetics/isolation &amp; purification ; *Genome, Viral ; Hominidae/virology ; High-Throughput Nucleotide Sequencing/methods ; Pan troglodytes/virology ; DNA, Viral/genetics ; Hepatitis B virus/genetics/isolation &amp; purification ; },
abstract = {Natural history museum collections harbour a record of wild species from the past centuries, providing a unique opportunity to study animals as well as their infectious agents. Thousands of great ape specimens are kept in these collections, and could become an important resource for studying the evolution of DNA viruses. Their genetic material is likely to be preserved in dry museum specimens, as reported previously for monkeypox virus genomes from historical orangutan specimens. Here, we screened 209 great ape museum specimens for 99 different DNA viruses, using hybridization capture coupled with short-read high-throughput sequencing. We determined the presence of multiple viruses within this dataset from historical specimens and obtained several near-complete viral genomes. In particular, we report high-coverage (> 18-fold) hepatitis B virus genomes from one gorilla and two chimpanzee individuals, which are phylogenetically placed within clades infecting the respective host species.},
}
@article {pmid39616151,
year = {2024},
author = {Wang, J and Zhong, H and Chen, Q and Ni, J},
title = {Adaption mechanism and ecological role of CPR bacteria in brackish-saline groundwater.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {141},
pmid = {39616151},
issn = {2055-5008},
support = {52070002, 51721006, 51925901//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52209078//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023T160020//China Postdoctoral Science Foundation/ ; },
mesh = {*Groundwater/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; *Phylogeny ; Salinity ; Biodiversity ; Metagenome ; Adaptation, Physiological ; Nitrogen/metabolism ; Carbon/metabolism ; Sulfur/metabolism ; Metagenomics/methods ; Bacterial Physiological Phenomena ; },
abstract = {Candidate phyla radiation (CPR) constitutes a substantial fraction of bacterial diversity, yet their survival strategies and biogeochemical roles in brackish-saline groundwater remain unknown. By reconstructing 399 CPR metagenome-assembled genomes (MAGs) and 2007 non-CPR MAGs, we found that CPR, affiliated with 44 previously proposed phyla and 8 putative novel phyla, played crucial roles in maintaining the microbial stability and complexity in groundwater. Metabolic reconstructions revealed that CPR participated in diverse processes, including carbon, nitrogen, and sulfur cycles. Adaption of CPR to high-salinity conditions could be attributed to abundant genes associated with heat shock proteins, osmoprotectants, and sulfur reduction, as well as their cooperation with Co-CPR (non-CPR bacteria co-occurred with CPR) for metabolic support and resource exchange. Our study enhanced the understanding of CPR biodiversity in high-salinity groundwater, highlighting the collaborative roles of self-adaptive CPR bacteria and their reciprocal partners in coping with salinity stress, maintaining ecological stability, and mediating biogeochemical cycling.},
}
@article {pmid39615696,
year = {2024},
author = {Li, Z and Zhang, Q and Lian, X and Yin, C and Lin, Y and Wang, Y and Han, Z and Shen, F and Xu, Y and Wang, H and Wang, T},
title = {Value of metagenomic next-generation sequencing in the diagnosis of native pyogenic spinal infections: a multicenter, retrospective observational study.},
journal = {The spine journal : official journal of the North American Spine Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.spinee.2024.11.004},
pmid = {39615696},
issn = {1878-1632},
abstract = {BACKGROUND CONTEXT: The etiological diagnosis of pyogenic spinal infection is crucial for its precise antibiotic treatment. Traditional methods of detection are often slow and ineffective. In recent times, metagenomic next-generation sequencing (mNGS) has revolutionized pathogen detection, offering a more effective approach to disease management.<br><br>PURPOSE: Comparing mNGS with microbial culture to comprehensively explore the diagnostic value of mNGS in pyogenic spinal infections.<br><br>DESIGN: A multicenter, retrospective observational study.<br><br>PATIENT SAMPLE: In a multicenter retrospective observational study, we analyzed the data from 301 patients admitted in 4 selected hospitals with pyogenic spinal infections from December 2019 to February 2024.<br><br>OUTCOME MEASURES: Identification of pathogenic bacteria in patients.<br><br>METHODS: Obtain blood and lesion tissue or pus samples from the enrolled patients for microbial culture, serological and hematological laboratory tests, pathological examination, and mNGS analysis, followed by a comparative analysis of the results.<br><br>RESULTS: In our cohort of 301 cases of clinically diagnosed pyogenic spinal infections, 242 yielded etiological evidence. The most common gram-positive bacterium was Staphylococcus aureus, and the most common gram-negative bacterium was Escherichia coli. mNGS showed a significantly higher rate of detection (77.9%) compared with microbial culture (27.2%) with a notable difference (X&#xb2;&#x202f;=&#x202f;140.17, P < 0.001). In culture-negative samples, mNGS could detect pathogens in 73.1% of cases, and in culture-positive samples, it could detect pathogens in 91.5% of cases with 94.7% genus-level concordance. mNGS provided faster results (24-48 h) compared with the culture method (2-7 days).<br><br>CONCLUSIONS: mNGS serves as a valuable supplement to the culture method and shows potential in identifying the causative pathogen in native pyogenic spinal infections.},
}
@article {pmid39615665,
year = {2024},
author = {Kurukulasooriya, MRP and Tillekeratne, LG and Wijayaratne, WMDGB and Bodinayake, CK and Dilshan, UHBY and De Silva, AD and Nicholson, BP and Østbye, T and Woods, CW and Nagahawatte, AS},
title = {Prevalence and molecular epidemiology of methicillin-resistant Staphylococcus aureus in livestock farmers, livestock, and livestock products in southern Sri Lanka: A one health approach.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105693},
doi = {10.1016/j.meegid.2024.105693},
pmid = {39615665},
issn = {1567-7257},
abstract = {Methicillin-resistant Staphylococcus aureus (MRSA) colonization can lead to subsequent severe infections. Unlike community and hospital-associated types, Livestock-associated MRSA (LA-MRSA) transmits to humans through direct contact with livestock and contaminated livestock products. This study aimed to investigate MRSA prevalence and molecular epidemiology in livestock farmers, livestock, and livestock products, including LA-MRSA presence and MRSA abundance in human and animal nasal microbiome, in southern Sri Lanka using a One Health approach. Nasal swabs from farmers and livestock on 50 farms (Nov 2020 - Dec 2021) and livestock products were collected. MRSA was isolated and confirmed using standard microbiological techniques. Staphylococcal chromosomal cassette mec typing, spa typing, and multilocus sequence typing were performed. Identified clones were compared with hospital isolates. Metagenomics analysis was performed on selected samples. MRSA prevalence was 24.0 % (12/50) in farms, 7.9 % (12/152) in farmers, 2.1 % (5/240) in livestock, and 1.9 % (3/157) in products. Of 372 S. aureus collected from clinical cultures, 59.4 % were MRSA. MRSA clones were identified in farm personnel (CC5/ST5/t002, CC1/ST1/t127, and ST45/CC45/t026), livestock (CC5/ST5/t002), and clinical cultures (CC5/ST5/t002 and CC5/ST6/t304), with ST45/CC45/t026 and CC5/ST6/t304 reported for the first time in Sri Lanka. LA-MRSA clones (ST389/ST9) were not detected. Animals had more diverse nasal microbiomes and lower MRSA abundance (<1.4 %) compared to humans (>82.3 %). MRSA colonization prevalence in southern Sri Lanka was relatively low. Two new clones and no LA-MRSA clones were identified. This study highlights the importance of continuing MRSA surveillance under the One Health framework to identify MRSA transmission between humans, animals, and the environment.},
}
@article {pmid39615467,
year = {2024},
author = {Khandeparker, L and Kale, D and Hede, N and Anil, AC},
title = {Application of functional metagenomics in the evaluation of microbial community dynamics in the Arabian Sea: Implications of environmental settings.},
journal = {Journal of environmental management},
volume = {373},
number = {},
pages = {123449},
doi = {10.1016/j.jenvman.2024.123449},
pmid = {39615467},
issn = {1095-8630},
abstract = {Ocean microbial communities form the base of marine food webs, facilitating energy transfer and nutrient cycling, thereby supporting higher trophic levels. We investigated their composition and functional profiles across depths (surface waters 0, 29, and 63 m and bottom waters 100, 150, and 200 m) in the central-eastern Arabian Sea (CEAS) using next-generation sequencing. It was hypothesized that the composition and functional diversity of these communities would be influenced by depth and environmental parameters. Our research showed that microbial communities vary with depth and are shaped by environmental factors like irradiance, temperature, dissolved oxygen, suspended particulate matter, chlorophyll a, and ammonia concentrations. Cyanobacteria (Prochlorococcus sp) and Mamiellaceae, belonging to picoeukaryotes, exhibited distinct depth-specific distributions up to subsurface chlorophyll maxima (SCM) at 63 m. On the other hand, a community shift in the microbial communities comprising Firmicutes, Bacteroidetes, and Actinobacteria phyla was observed at the deeper water depths. The profiling of functional genes pointed out the expression of carbon fixation by photosynthetic organisms at the surface (0, 29, and 63 m), which shifted to prokaryotic carbon fixation in deeper waters (0, 150, and 200 m). Microcosm experiments (mixing of surface water with water from the SCM) carried out simulating disturbances such as climate change forced mixing (cyclones), revealed shifts in microbial structure and function. It was observed that within 48 h, the carbon fixation activity changed from photosynthetic organisms to prokaryotes and indicated an increase in stress-related biosynthetic pathways such as expression of quorum sensing, biosynthesis of antibiotics, lipopolysaccharides, and secondary metabolites. These findings have implications for predictive modelling of food web dynamics and fisheries management in the context of climate change.},
}
@article {pmid39615200,
year = {2024},
author = {Wang, J and Zhang, F and Wang, Z and Liang, H and Du, Z and Zhang, Y and Lu, H and Peng, Y},
title = {Metagenomic insights into nitrite accumulation in sulfur-based denitrification systems utilizing different electron donors: Functional microbial communities and metabolic mechanisms.},
journal = {Water research},
volume = {270},
number = {},
pages = {122805},
doi = {10.1016/j.watres.2024.122805},
pmid = {39615200},
issn = {1879-2448},
abstract = {Sulfur-based autotrophic denitrification (SADN) offers new pathway for nitrite supply. However, sequential transformation of nitrogen and sulfur forms, and the functional microorganisms driving nitrite accumulation in SADN with different reduced inorganic sulfur compounds (RISCs), remain unclear. Desirable nitrite accumulation was achieved using elemental sulfur (S[0]-group), sulfide (S[2-]-group) and thiosulfate (S2O3[2-]-group) as electron donors. Under equivalent electron supply conditions, S2O3[2-]-group exhibited a superior nitrate conversion rate (NCR) of 0.285 kg N/(m[3]·d) compared to S[2-]-group (0.103 kg N/(m[3]·d)). Lower NCR in S[2-]-group was attributed to sulfide strongly inhibiting energy metabolism process of TCA cycle, resulting in reduced reaction rates. Moreover, the NCR of S[0]-group (0.035 kg N/(m[3]·d)) was poor due to the chemical inertness of S[0]. Specific microbial communities were selectively enriched in phylum level, with Proteobacteria increasing to an astonished 96.27-98.49 %. Comprehensive analyses of functional genus, genes, and metabolic pathways revealed significant variability in the active functional genus, with even the same genus showed significant metabolic differences in response to different RISCs. In S[0]-group, Thiomonas (10.0 %) and Acidithiobacillus (5.1 %) were the primary contributor to nitrite accumulation. Thiobacillus was the most abundant sulfur-oxidizing bacteria in S[2-]-group (43.84 %) and S2O3[2-]-group (18.92 %). In S[2-]-group, it contributed to nitrite accumulation, while in S2O3[2-]-group, it acted as a complete denitrifier (NO3[-]-N→N2). Notably, heterotrophic denitrifying bacteria, Comamonas (12.52 %), were crucial for nitrite accumulation in S2O3[2-]-group, predominating NarG while lacking NirK/S. Overall, this work advances our understanding of SADN systems with different RISCs, offering insights for optimizing nitrogen and sulfur removal.},
}
@article {pmid39615045,
year = {2024},
author = {Valentino, V and De Filippis, F and Marotta, R and Pasolli, E and Ercolini, D},
title = {Genomic features and prevalence of Ruminococcus species in humans are associated with age, lifestyle, and disease.},
journal = {Cell reports},
volume = {43},
number = {12},
pages = {115018},
doi = {10.1016/j.celrep.2024.115018},
pmid = {39615045},
issn = {2211-1247},
abstract = {The genus Ruminococcus is dominant in the human gut, but higher levels of some species, such as R. gnavus, R. torques, and R. bromii, have been linked to health or disease. In this study, we analyzed >9,000 Ruminococcus metagenome-assembled genomes (MAGs) reconstructed from >5,000 subjects and revealed significant links between the prevalence of some species/subspecies and geographic origin, age, lifestyle, and disease, with subspecies prevalent in specific subpopulations showing divergent metabolic potential. Furthermore, Ruminococcus species from Lachnospiraceae encoded for carbohydrate-active enzymes (CAZy) potentially involved in the metabolism of human N- and O-glycans, whereas those from Oscillospiraceae appear to be more adapted toward fiber metabolism. These new findings contribute to elucidating the potential functional role of Ruminococcus in specific lifestyles and diseases and to decipher the diversity and the adaptation of members of this genus to the human gut.},
}
@article {pmid39614549,
year = {2024},
author = {Wicaksono, WA and Akinyemi, OE and Wassermann, B and Bickel, S and Suwanto, A and Berg, G},
title = {Traditionally produced tempeh harbors more diverse bacteria with more putative health-promoting properties than industrially produced tempeh.},
journal = {Food research international (Ottawa, Ont.)},
volume = {196},
number = {},
pages = {115030},
doi = {10.1016/j.foodres.2024.115030},
pmid = {39614549},
issn = {1873-7145},
mesh = {*Bacteria/genetics/classification/metabolism ; *Food Microbiology ; Humans ; Soy Foods/microbiology ; Fermentation ; Rhizopus/genetics/metabolism ; Hygiene ; Indonesia ; Microbiota ; Fermented Foods/microbiology ; },
abstract = {In recent years, there has been a significant shift towards industrialization in food production, resulting in the implementation of higher hygiene standards globally. Our study focused on examining the impact of hygiene standards on tempeh, a popular Rhizopus-based fermented soybean product native to Indonesia, and now famous around the world. We observed that tempeh produced with standardized hygiene measures exhibited a microbiome with comparable bacterial abundances but a markedly different community structure and function than traditionally produced tempeh. In detail, we found a decreased bacterial abundance of lactobacilli and enterobacteria, bacterial diversity, different indicator taxa, and significantly changed community structure in industrial tempeh. A similar picture was found for functional analysis: the quantity of bacterial genes was similar but qualitative changes were found for genes associated with human health. The resistome of tempeh varied based on its microbiome composition. The higher number of antimicrobial resistance genes in tempeh produced without standardized hygiene measures mainly belong to multidrug efflux pumps known to occur in plant-based food. Our findings were confirmed by functional insights into genomes and metagenome-assembled genomes from the dominant bacteria, e.g. Leuconostoc, Limosilactobacillus, Lactobacillus, Enterococcus, Paenibacillus, Azotobacter and Enterobacter. They harboured an impressive spectrum of genes important for human health, e.g. for production of vitamin B1, B7, B12, and K, iron and zinc transport systems and short chain fatty acid production. In conclusion, industrially produced tempeh harbours a less diverse microbiome than the traditional one. Although this ensures production at large scales as well as biosafety, in the long-term it can lead to potential effects for human gut health.},
}
@article {pmid39614478,
year = {2024},
author = {Yu, H and Li, Z and Zheng, D and Chen, C and Ge, C and Tian, H},
title = {Exploring microbial dynamics and metabolic pathways shaping flavor profiles in Huangjiu through metagenomic analysis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {196},
number = {},
pages = {115036},
doi = {10.1016/j.foodres.2024.115036},
pmid = {39614478},
issn = {1873-7145},
mesh = {*Taste ; *Metagenomics/methods ; *Fermentation ; *Wine/microbiology/analysis ; *Metabolic Networks and Pathways ; Microbiota/genetics ; Oryza/microbiology ; Flavoring Agents/metabolism ; Humans ; Food Microbiology ; Odorants/analysis ; Male ; },
abstract = {In the production of Huangjiu (Chinese rice wine), fermentation microbiota plays a crucial role in flavor formation. This study investigates the microbial dynamics and metabolic pathways that shape the flavor profiles of Huangjiu using different starters. Sensory evaluation and metabolite analysis of six starters revealed significant differences in ester, fruity, and sweet aromas. Saccharomyces, Aspergillus, and Rhizopus were identified as the dominant genera significantly impacting fermentation. Metagenomic species and functional gene annotations of Huangjiu starters elucidated the metabolic pathways for key flavor compounds synthesis pathways. Enzyme genes involved in these pathways were classified and annotated to microbial genera using the NR database, identifying 231 classes of relevant catalytic enzymes and 154 microbial genera. A metabolic relationship between flavor compound formation and different microbial genera was established using catalytic enzymes as a bridge. This study highlights the impact of starter composition on the final product and provides new insights for optimizing starters to enhance Huangjiu flavor quality.},
}
@article {pmid39614477,
year = {2024},
author = {Yang, L and Fan, W and Xu, Y},
title = {Effects of storage period and season on the microecological characteristics of Jiangxiangxing high-temperature Daqu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {196},
number = {},
pages = {115034},
doi = {10.1016/j.foodres.2024.115034},
pmid = {39614477},
issn = {1873-7145},
mesh = {*Seasons ; *Hot Temperature ; *Food Storage/methods ; *Microbiota ; Fermentation ; Bacteria/metabolism/classification ; Food Microbiology ; Metabolomics ; Proteomics ; China ; Metagenomics ; Camellia sinensis/microbiology/metabolism ; Fungi/metabolism/classification ; },
abstract = {Metagenomics, non-targeted metabolomics, and metaproteomics were employed to analyze the microecological succession of high-temperature Daqu during storage, elucidate the adaptation mechanism of the microbial community of Daqu to storage environments, and clarify the microecological characteristics of Daqu during different seasons. During storage, the relative abundances of Bacillus, Oceanobacillus, Staphylococcus, and Aspergillus in Daqu had significantly increased, while those of Kroppenstedtia, Saccharopolyspora, Thermoascus, and Thermomyces had significantly decreased. During the first 3 months of storage, compound metabolism of Daqu was primarily dominated by generation of small molecular substances and then shifted to metabolism of amino sugars. During the storage process, homogeneous selection (15.57 %) and homogeneous diffusion (14.86 %) of the microbial communities of Daqu were much larger than during the fermentation process, while the variable selection assembly (29.43 %) was smaller than during the fermentation process. Among the 2509 proteins identified in the four-season Daqu, bacterial protein expression was 1.46-fold greater than that of fungi. Seasonal factors influenced the function of Daqu by alterations to Bacillus subtilis, Oceanobacillus iheyensis, and Aspergillus nidulans and other microbial functions. Carbon and benzoic acid metabolism of Daqu was relatively increased during the spring, while metabolism of alkaloids and tyrosine was upregulated during the summer, amino acid synthesis and starch metabolism were enriched during the autumn, and peptidoglycan synthesis was relatively greater during the winter. Adjusting the moisture content of Daqu during the storage period was shown to reduce microecological differentiation caused by seasonal temperature variations.},
}
@article {pmid39614390,
year = {2024},
author = {Lai, Y and Zhou, F and Wang, H and He, X and Zhang, Q and Zhou, Y},
title = {Application of bronchoalveolar lavage fluid cytomorphology in diagnosing Nocardia otitidiscaviarum: a case report.},
journal = {Journal of medical case reports},
volume = {18},
number = {1},
pages = {577},
pmid = {39614390},
issn = {1752-1947},
support = {220906053235359//2022 Ministry of Education Industry-University Cooperation Collaborative Education Project/ ; 2021WJCY090//Hangzhou Biomedicine and Health Industry Development Supporting Science and Technology Special Project (Phase III, 2021)/ ; 2021WJCY272//Hangzhou Biomedicine and Health Industry Development Supporting Science and Technology Special Project (Phase V, 2021)/ ; },
mesh = {Humans ; Male ; *Nocardia Infections/diagnosis/microbiology/drug therapy ; Aged ; *Bronchoalveolar Lavage Fluid/microbiology ; *Nocardia/isolation &amp; purification ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {BACKGROUND: Nocardiosis is a rare infectious disease, which is frequently underdiagnosed because of the distinct bacterial shape of the causative agent and its developmental history. The morphological analysis of bronchoalveolar lavage fluid can facilitate the detection of pathogenic bacteria by observing cellular-bacterial interactions.<br><br>CASE PRESENTATION: An immunocompetent 67-year-old male patient of Asian ethnicity developed a cough without apparent cause 20&#xa0;days earlier. We initially discovered mycobacteria that appeared to be Nocardia in the cytomorphological examination of bronchoalveolar lavage fluid, which was later determined to be Nocardia otitidiscaviarum through metagenomic next-generation sequencing and microbiological cultures. The patient was eventually diagnosed with Nocardia pneumonitis after other testing and clinical signs were considered. After anti-infective treatment, the patient improved and was discharged.<br><br>CONCLUSION: Several diagnostic approaches were used in this case, and the importance of cell morphology as an early screening method was emphasized for suspected Nocardia infection.},
}
@article {pmid39614169,
year = {2024},
author = {Tang, H and Du, S and Niu, Z and Zhang, D and Tang, Z and Chen, H and Chen, Z and Zhang, M and Xu, Y and Sun, Y and Fu, X and Norback, D and Shao, J and Zhao, Z},
title = {Nasal, dermal, oral and indoor dust microbe and their interrelationship in children with allergic rhinitis.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {505},
pmid = {39614169},
issn = {1471-2180},
mesh = {Humans ; *Dust/analysis ; Male ; Child ; Female ; *Rhinitis, Allergic/microbiology ; Case-Control Studies ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/isolation &amp; purification/genetics ; *Skin/microbiology ; *Mouth/microbiology ; *Microbiota ; Nasal Cavity/microbiology ; Air Pollution, Indoor/analysis ; Child, Preschool ; Metagenomics/methods ; Nose/microbiology ; },
abstract = {BACKGROUND: Allergic rhinitis (AR) subjects might have their microenvironment changed due to pathogenesis and living environment. Whether the nasal microbe in AR children differs from healthy subjects and how it interplays with dermal, oral and indoor dust microbe needs to be elucidated.<br><br>METHODS: In this case-control study, we analyzed and compared the bacterial characterization and associations in nasal, dermal, oral swab samples and dust samples in 62 children with physician-diagnosed AR(cases) and 51 age- and gender-matched healthy ones with no history of allergic diseases(controls). Full-length 16S rRNA sequencing(swabs) and shotgun metagenomics(dust) were applied. Bacterial diversity, composition, abundance difference characteristics and fast expectation-maximization for microbial source tracking(FEAST) analysis were performed and compared between cases and controls.<br><br>RESULTS: The &#x3b1;-diversity of dust microorganisms in AR was lower than that in control group (P&#x2009;=&#x2009;0.034), and the &#x3b2;-diversity indices of microorganisms in nasal cavity (P&#x2009;=&#x2009;0.020), skin (P&#x2009;=&#x2009;0.001) and dust (P&#x2009;=&#x2009;0.004) were significantly different from those in control group. At species levels, a total of 10, 15, 12, and 15 bacterial species were differentially enriched in either cases or controls in nasal, dermal, oral, and dust samples, respectively(Linear Discriminant Analysis(LDA) score&#x2009;>&#x2009;2, P&#x2009;<&#x2009;0.05). Staphylococcus epidermidis was the single species simultaneously more abundant in nasal, dermal and dust samples in AR children. By FEAST analysis, 8.85% and 10.11% of S. epidermidis in AR dermal and dust samples came from nasal cavity. These proportions were significantly higher than those in controls (2.70% and 3.86%) (P&#x2009;<&#x2009;0.05). The same significantly higher transfer proportions(P&#x2009;<&#x2009;0.05) were observed for Staphylococcus aureus enriched in the nasal cavity in AR children. Classification models by random forest regression at species levels showed, bacterial species enriched in indoor dust, nasal and dermal samples had substantial power in distinguishing AR children from healthy ones, with the highest power in the dust samples (AUC&#x2009;=&#x2009;0.88) followed by nasal(AUC&#x2009;=&#x2009;0.81) and dermal ones(AUC&#x2009;=&#x2009;0.80).<br><br>CONCLUSIONS: Our study presented the microbial enrichment characteristics in AR children both in the living environment(dust) and body sites exposed to environment through inhalation(nasal cavity), contact(skin) and ingestion(oral cavity) pathways, respectively. Nasal S.epidermidis and S.aureus had dominant influences on dust and other body sites in AR children.},
}
@article {pmid39614167,
year = {2024},
author = {Mangoma, N and Zhou, N and Ncube, T},
title = {Metagenomic insights into the microbial community of the Buhera soda pans, Zimbabwe.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {510},
pmid = {39614167},
issn = {1471-2180},
mesh = {Zimbabwe ; *Metagenomics ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Microbiota/genetics ; Salinity ; Phylogeny ; Hydrogen-Ion Concentration ; Archaea/genetics/classification/metabolism/isolation &amp; purification ; Water Microbiology ; },
abstract = {BACKGROUND: Soda pans are unique, natural aquatic environments characterised by elevated salinity and alkalinity, creating a distinctive and often extreme geochemistry. The microbiomes of soda pans are unique, with extremophiles such as halophiles, alkaliphiles and haloalkaliphiles being important. Despite being dominated by mostly unculturable inhabitants, soda pans hold immense biotechnological potential. The application of modern "omics-based" techniques helps us better understand the ecology and true extend of the biotechnological potential of soda pan microbiomes. In this study, we used a shotgun metagenomic approach to determine the microbial diversity and functional profile of previously unexplored soda pans located in Buhera, Eastern Zimbabwe. A combination of titrimetry and inductively coupled plasma optical emission spectroscopy (ICP‒OES) was used to perform physico-chemical analysis of the soda pan water.<br><br>RESULTS: Physicochemical analysis revealed that the Buhera soda pans are highly alkaline, with a pH range of 8.74 to 11.03, moderately saline (2.94 - 7.55 g/L), and have high carbonate (3625 mg/L) and bicarbonate ion (1325 mg/L) alkalinity. High levels of sulphate, phosphate, chloride and fluoride ions were detected. Metagenomic analysis revealed that domain Bacteria dominated the soda pan microbial community, with Pseudomonadota and Bacillota being the dominant phyla. Vibrio was shown to be the predominant genus, followed by Clostridium, Candidatus Brevefilum, Acetoanaerobium, Thioalkalivibrio and Marinilactibacillus. Archaea were also detected, albeit at a low prevalence of 1%. Functional profiling revealed that the Buhera soda pan microbiome is functionally diverse, has hydrolytic-enzyme production potential and is capable of supporting a variety of geochemical cycles.<br><br>CONCLUSIONS: The results of this pioneering study showed that despite their extreme alkalinity and moderate salinity, the Buhera soda pans harbour a taxonomically and functionally diverse microbiome dominated by bacteria. Future work will aim towards establishing the full extent of the soda pan's biotechnological potential, with a particular emphasis on potential enzyme production.},
}
@article {pmid39613370,
year = {2024},
author = {Zepernick, BN and Hart, LN and Chase, EE and Natwora, KE and Obuya, JA and Olokotum, M and Houghton, KA and Kiledal, EA and , and Sheik, CS and Sherman, DH and Dick, GJ and Wilhelm, SW and Sitoki, L and Otiso, KM and McKay, RML and Bullerjahn, GS},
title = {Molecular investigation of harmful cyanobacteria reveals hidden risks and niche partitioning in Kenyan Lakes.},
journal = {Harmful algae},
volume = {140},
number = {},
pages = {102757},
doi = {10.1016/j.hal.2024.102757},
pmid = {39613370},
issn = {1878-1470},
mesh = {*Lakes/microbiology ; *Cyanobacteria/genetics ; Kenya ; *Harmful Algal Bloom ; },
abstract = {Despite the global expansion of cyanobacterial harmful algal blooms (cHABs), research is biased to temperate systems within the global north, such as the Laurentian Great Lakes. This lack of diversity represents a significant gap in the field and jeopardizes the health of those who reside along at-risk watersheds in the global south. The African Great Lake, Lake Victoria, is understudied despite serving as the second largest lake by surface area and demonstrating year-round cHABs. Here, we address this knowledge gap by performing a molecular survey of cHAB communities in three anthropogenically and ecologically important freshwater systems of Victoria's Kenyan watershed: Winam Gulf (Lake Victoria), Lake Simbi and Lake Naivasha. We identified a bloom of non-toxic Dolichospermum and toxic Microcystis in the Winam Gulf, with data suggesting sulfur limitation shapes competition dynamics between these two bloom-formers. Though we did not detect a bloom in Naivasha, it contained the largest diversity of cHAB genera amongst the three lakes. In turn, our results indicated methane metabolism may allow non-toxic picoplankton to outcompete cHAB genera, while suggesting Synechococcus spp. serves as a methane source and sink in this system. Lake Simbi exhibited a non-toxic Limnospira bloom at the time of sampling with very low abundances of cHAB genera present. Subsequently, these results were employed to design a cHAB screening and risk assessment framework for local stakeholders. Cumulatively, this work serves to increase cHAB research efforts on the international scale while serving as an impetus for cHAB monitoring on the local scale.},
}
@article {pmid39612873,
year = {2024},
author = {Chen, M and Liu, Y and Zhou, Y and Pei, Y and Qu, M and Lv, P and Zhang, J and Xu, X and Hu, Y and Wang, Y},
title = {Deciphering antibiotic resistance genes and plasmids in pathogenic bacteria from 166 hospital effluents in Shanghai, China.},
journal = {Journal of hazardous materials},
volume = {483},
number = {},
pages = {136641},
doi = {10.1016/j.jhazmat.2024.136641},
pmid = {39612873},
issn = {1873-3336},
abstract = {Although previous studies using phenotypic or metagenomic approaches have revealed the patterns of antibiotic resistance genes (ARGs) in hospital effluents in local regions, limited information is available regarding the antibiotic resistome and plasmidome in human pathogenic bacteria in hospital effluents of megacity in China. To address this knowledge gap, we analyzed effluent samples from 166 hospitals across 13 geographical districts in Shanghai, China, using both cultivation-based approaches and metagenomics. A total of 357 strains were isolated from these samples, with the predominant species being Escherichia coli (n = 61), Aeromonas hydrophila (n = 57), Klebsiella pneumoniae (n = 48), and Aeromonas caviae (n = 42). Those identified indicator bacteria were classified into biosafety level 1 (BSL-1, 60 %) and BSL-2 (40 %). We identified 1237 ARG subtypes across 22 types, predominantly including beta-lactam, tetracycline, multidrug, polymyxin, and aminoglycoside resistance genes, using culture-enriched phenotypic metagenomics. Mobile genetic elements such as plasmids, transposons (tnpA), integrons (intI1), and insertion sequences (IS91) were abundant. We recovered 135 plasmids classified into mobilizable (n = 94) and non-mobilizable (n = 41) types. Additionally, 80 metagenome-assembled genomes (MAGs) were reconstructed from the hospital effluents for the assessment of ARG transmission risks, including genes for last-line antibiotics such as blaNDM, blaKPC, blaimiH, and mcr. This study is the first to comprehensively characterize and assess the risk of antimicrobial resistance levels and plasmidome in the hospital effluents of China's megacity, providing city-wide surveillance data and evidence to inform public health interventions.},
}
@article {pmid39612821,
year = {2024},
author = {Rosenqvist, T and Hilding, J and Suarez, C and Paul, CJ},
title = {Microbial communities in slow sand filters for drinking water treatment adapt to organic matter altered by ozonation.},
journal = {Water research},
volume = {270},
number = {},
pages = {122843},
doi = {10.1016/j.watres.2024.122843},
pmid = {39612821},
issn = {1879-2448},
abstract = {Changing natural organic matter quality from anthropogenic activity and stricter requirements for micropollutant removal challenges existing systems for drinking water production. Ozonation of water followed by biofiltration, such as passage through a slow sand filter (SSF), is a partial solution. Biofiltration relies on biofilms (microbial communities within extracellular matrices). However, the effects of ozonation on SSF microbial communities are unknown. In this study, genome-resolved and read-based metagenomics were used to compare the microbial communities of two full-scale SSFs employing conventional pre-treatment to a 20 m[2] SSF operated in parallel with ozonation as additional pre-treatment. The SSF microbial community receiving ozonated water was less diverse than those receiving non-ozonated water. Families Hyphomicrobiaceae, Acetobacteraceae, Sphingomonadaceae and Burkholderiaceae were more abundant when ozone was used, as were genes for metabolism of single-carbon organic compounds. Conversely, genes for metabolism of aromatic compounds and fatty acids were less abundant. Metagenome assembled genomes associated with the non-ozonated SSFs were enriched with several glycoside hydrolases, while those associated with the ozonated SSF were enriched with genes for 1-2 carbon compound metabolism. No indications of increased microbial risk (pathogens or antibiotic resistance genes) were detected as a consequence of ozonation. This study shows how microbial communities of SSFs adapt to changes in organic matter quality, highlighting the key role of biofilters for production of safe and sustainable drinking water in a changing climate.},
}
@article {pmid39612230,
year = {2024},
author = {Zhang, Z and Yu, S and Gu, J and Tan, F and Wan, S and Gao, H and Qin, Z},
title = {Biochemical Characterization of a β-1,3-Glucanase from Bacteroidetes sp. Having Transglycosylase Activity Suitable to Synthesize β-Glucooligosaccharides.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c08008},
pmid = {39612230},
issn = {1520-5118},
abstract = {β-1,3-Glucanases have prospective applications in areas such as functional oligosaccharide preparation, plant protection, and breweries. In this study, a glycoside hydrolase (GH) family 17 β-1,3-glucanase (BbGlc17A) from Bacteroidetes bacterium from a microbial mat metagenome from the Great Salt Lake was identified. BbGlc17A catalyzed the hydrolytic conversion of laminarin into β-glucooligosaccharides with polymerization degrees of 3-8. The optimal catalytic conditions of BbGlc17A were pH 6.5 and 30 °C. In addition to its hydrolytic activity, BbGlc17A also exhibited transglycosidase activities, involving catalysis of the formation of new β-1,6-glycosidic bonds. BbGlc17A exhibits the classic (β/α)8 TIM-barrel structure and possesses an elongated catalytic groove, distinguishing it from other typical β-1,3-glucanases, which promote the forward direction of the transglycoside reaction. This effectively highlights the potential of the enzyme to convert β-1,3-glucan into mixed functional oligosaccharides. These results reveal the catalytic properties and the application potential of the GH family 17 β-1,3-glucanase and provide valuable information about the group of carbohydrate-active enzymes in biochemistry.},
}
@article {pmid39612216,
year = {2024},
author = {Wang, T and Luo, Y and Kong, X and Fang, L and Zhu, L and Yu, B and Zheng, P and Huang, Z and Mao, X and Jie, Y and Luo, J and Yan, H and He, J},
title = {Multiomics comparative analysis of feces AMRGs of Duroc pigs and Tibetan and the effect of fecal microbiota transplantation on AMRGs upon antibiotic exposure.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0198324},
doi = {10.1128/spectrum.01983-24},
pmid = {39612216},
issn = {2165-0497},
abstract = {UNLABELLED: Fecal matter is recognized as both a reservoir and a transmission source for various antimicrobial resistance genes (AMRGs). However, the transcriptional activity of AMRGs in swine feces is not well understood. In addition, the effect of fecal microbiota transplantation (FMT) on the excretion of AMRGs has rarely been reported. Our study explored the diversity, abundance, transcriptional activity, and bacterial hosts of AMRGs in Tibetan and Duroc pig feces using metagenomic and metatranscriptomic sequencing technologies. We discovered a significantly higher genomic abundance of AMRGs in the feces of Duroc pigs compared to Tibetan pigs (P < 0.001), although the transcript levels did not show a significant difference. The results showed that the core composition of AMRGs in pig feces varied considerably, with the most transcriptionally active AMRGs being oqxB, tetQ, Bla1, dfrA1, and amrB. Furthermore, the Firmicutes phylum is the main host of AMRGs. By transplanting fecal flora from Tibetan and Duroc pigs into the intestines of Duroc Landrace Yorkshire (DLY) piglets after acute antibiotic exposure, we found that only Tibetan pig fecal flora significantly reduced AMRGs in the feces of DLY piglets (P < 0.05). The effectiveness of Tibetan pig fecal microorganisms in removing AMRGs from DLY pig feces was mainly influenced by microbial communities, especially the Bacteroidota phylum. These findings offer valuable insights for the prevention and control of AMRG pollution.<br><br>IMPORTANCE: To the best of our knowledge, this study represents the first comprehensive analysis of antimicrobial resistance gene (AMRGs) expression in the fecal microbiota of Tibetan and Duroc pigs, employing an integrated metagenomic and metatranscriptomic approach. Our findings indicate a higher risk of AMRGs transmission in the feces of Duroc pigs compared to Tibetan pigs. Given the escalating antimicrobial resistance crisis, novel therapeutic interventions are imperative to mitigate gut colonization by pathogens and AMRGs. In this regard, we investigated the impact of fecal microbiota from Tibetan and Duroc pig sources on AMRGs excretion in Duroc Landrace Yorkshire (DLY) piglets' feces following acute antibiotic exposure. Remarkably, only fecal microbiota sourced from Tibetan pigs exhibited a reduction in AMRGs excretion in DLY piglets' feces. This underscores the significance of evaluating the presence of AMRGs within donor fecal microbiota for effective AMRGs decolonization strategies.},
}
@article {pmid39611829,
year = {2024},
author = {Hameed, A and McDonagh, F and Sengupta, P and Miliotis, G and Sivabalan, SKM and Szydlowski, L and Simpson, A and Singh, NK and Rekha, PD and Raman, K and Venkateswaran, K},
title = {Neobacillus driksii sp. nov. isolated from a Mars 2020 spacecraft assembly facility and genomic potential for lasso peptide production in Neobacillus.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0137624},
doi = {10.1128/spectrum.01376-24},
pmid = {39611829},
issn = {2165-0497},
abstract = {UNLABELLED: During microbial surveillance of the Mars 2020 spacecraft assembly facility, two novel bacterial strains, potentially capable of producing lasso peptides, were identified. Characterization using a polyphasic taxonomic approach, whole-genome sequencing and phylogenomic analyses revealed a close genetic relationship among two strains from Mars 2020 cleanroom floors (179-C4-2-HS, 179-J1A1-HS), one strain from the Agave plant (AT2.8), and another strain from wheat-associated soil (V4I25). All four strains exhibited high 16S rRNA gene sequence similarity (>99.2%) and low average nucleotide identity (ANI) with Neobacillus niacini NBRC 15566[T], delineating new phylogenetic branches within the genus. Detailed molecular analyses, including gyrB (90.2%), ANI (86.4%), average amino acid identity (87.8%) phylogenies, digital DNA-DNA hybridization (32.6%), and percentage of conserved proteins (77.7%) indicated significant divergence from N. niacini NBRC 15566[T]. Consequently, these strains have been designated Neobacillus driksii sp. nov., with the type strain 179-C4-2-HS[T] (DSM 115941[T] = NRRL B-65665[T]). N. driksii grew at 4°C to 45°C, pH range of 6.0 to 9.5, and 0.5% to 5% NaCl. The major cellular fatty acids are iso-C15:0 and anteiso-C15:0. The dominant polar lipids include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unidentified aminolipid. Metagenomic analysis within NASA cleanrooms revealed that N. driksii is scarce (17 out of 236 samples). Genes encoding the biosynthesis pathway for lasso peptides were identified in all N. driksii strains and are not commonly found in other Neobacillus species, except in 7 out of 26 recognized species. This study highlights the unique metabolic capabilities of N. driksii, underscoring their potential in antimicrobial research and biotechnology.<br><br>IMPORTANCE: The microbial surveillance of the Mars 2020 assembly cleanroom led to the isolation of novel N. driksii with potential applications in cleanroom environments, such as hospitals, pharmaceuticals, semiconductors, and aeronautical industries. N. driksii genomes were found to possess genes responsible for producing lasso peptides, which are crucial for antimicrobial defense, communication, and enzyme inhibition. Isolation of N. driksii from cleanrooms, Agave plants, and dryland wheat soils, suggested niche-specific ecology and resilience under various environmentally challenging conditions. The discovery of potent antimicrobial agents from novel N. driksii underscores the importance of genome mining and the isolation of rare microorganisms. Bioactive gene clusters potentially producing nicotianamine-like siderophores were found in N. driksii genomes. These siderophores can be used for bioremediation to remove heavy metals from contaminated environments, promote plant growth by aiding iron uptake in agriculture, and treat iron overload conditions in medical applications.},
}
@article {pmid39611823,
year = {2024},
author = {Carroll, AC and Mortimer, L and Ghosh, H and Reuter, S and Grundmann, H and Brinda, K and Hanage, WP and Li, A and Paterson, A and Purssell, A and Rooney, A and Yee, NR and Coburn, B and Able-Thomas, S and Antonio, M and McGeer, A and MacFadden, DR},
title = {Rapid inference of antibiotic susceptibility phenotype of uropathogens using metagenomic sequencing with neighbor typing.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0136624},
doi = {10.1128/spectrum.01366-24},
pmid = {39611823},
issn = {2165-0497},
abstract = {UNLABELLED: Timely diagnostic tools are needed to improve antibiotic treatment. Pairing metagenomic sequencing with genomic neighbor typing algorithms may support rapid clinically actionable results. We created resistance-associated sequence elements (RASE) databases for Escherichia coli and Klebsiella spp. and used them to predict antibiotic susceptibility in directly sequenced (Oxford Nanopore) urine specimens from critically ill patients. RASE analysis was performed on pathogen-specific reads from metagenomic sequencing. We evaluated the ability to predict (i) multi-locus sequence type (MLST) and (ii) susceptibility profiles. We used neighbor typing to predict MLST and susceptibility phenotype of E. coli (64/80) and Klebsiella spp. (16/80) from urine samples. When optimized by lineage score, MLST predictions were concordant for 73% of samples. Similarly, a RASE-susceptible prediction for a given isolate was associated with a specificity and a positive likelihood ratio (LR+) for susceptibility of 0.65 (95% CI, 0.54-0.76) and 2.26 (95% CI, 1.75-2.92), respectively, with an increase in the probability of susceptibility of 10%. A RASE-non-susceptible prediction was associated with a sensitivity and a negative likelihood ratio (LR-) for susceptibility of 0.79 (95% CI, 0.74-0.84) and 0.32 (95% CI, 0.24-0.43) respectively, with a decrease in the probability of susceptibility of 20%. Numerous antibiotic classes could reasonably be reconsidered empiric therapy by shifting empiric probabilities of susceptibility across relevant treatment thresholds. Moreover, these predictions can be available within 6 h. Metagenomic sequencing of urine specimens with neighbor typing provides rapid and informative predictions of lineage and antibiotic susceptibility with the potential to impact clinical decision-making.<br><br>IMPORTANCE: Urinary tract infections (UTIs) are a common diagnosis in hospitals and are often treated empirically with broad-spectrum antibiotics. These broad-spectrum agents can select for resistance in these bacteria and co-colonizing organisms. The use of narrow-spectrum agents is desirable as an antibiotic stewardship measure; however, it is counterbalanced by the need for adequate therapy. Identification of causative organisms and their antibiotic susceptibility can help direct treatment; however, conventional testing requires days to produce actionable results. Methods to quickly and accurately predict susceptibility phenotypes for pathogens causing UTI could thus improve both patient outcomes and antibiotic stewardship. Here, expanding on previous work showing accurate prediction for certain Gram-positive pathogens, we demonstrate how the use of RASE from metagenomic sequencing can provide informative and rapid phenotype prediction results for common Gram-negative pathogens in UTI, highlighting the future potential of this method to be used in clinical settings to guide empiric antibiotic selection.},
}
@article {pmid39611812,
year = {2024},
author = {Shi, M and Zhao, B and Cai, W and Yuan, H and Liang, X and Li, Z and Liu, X and Jin, Y and Liu, X and Wei, C},
title = {Multi-omics mechanical analysis of gut microbiota, carboxylic acids, and cardiac gene expression interaction triggering diabetic cardiomyopathy.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0145024},
doi = {10.1128/msystems.01450-24},
pmid = {39611812},
issn = {2379-5077},
abstract = {UNLABELLED: It is well known that gut microbial imbalance is a potential factor for the occurrence and development of diabetes mellitus (DM) and its complications. Moreover, the heart and gut microbiota can regulate each other through the gut-metabolite-heart axis. In this study, metagenomics, metabolomics, and transcriptomics were chosen to sequence the changes in gut microbiota, serum metabolite levels, and differentially expressed genes (DEGs) in leptin receptor-deficient db/db mice and analyze the correlation between serum metabolites and gut microbiota or DEGs. According to the results, there were significant differences in the 1,029 cardiac genes and 353 serum metabolites in diabetic mice of the db/db group, including DEGs enriched in the PPAR signaling pathway and increased short-chain carboxylic acids (CAs), when compared with the normal db/m group. According to metagenomics, the gut microbiota of mice in the db/db group were disrupted, and particularly Lachnospiraceae bacteria and Oscillospiraceae bacteria significantly decreased. Also, according to the Pearson correlation analysis, a significant positive correlation was found between CAs and PPAR signaling pathway-related DEGs, and a negative correlation was found between CAs and the abundance of the above-mentioned species. To sum up, type 2 diabetes mellitus (T2DM) can upregulate the expression of partial cardiac genes through the levels of serum short-chain CAs affected by gut microbiota, thus playing a role in the occurrence and development of diabetic cardiomyopathy (DCM).<br><br>IMPORTANCE: Our research results clearly link the changes in heart genes of T2DM and normal mice with changes in serum metabolites and gut microbiota, indicating that some genes in biological processes are closely related to the reduction of protective microbiota in the gut microbiota. This study provides a theoretical basis for investigating the mechanism of DCM and may provide preliminary evidence for the future use of gut microbiota therapy for DCM.},
}
@article {pmid39611384,
year = {2025},
author = {Redding, LE and Daniel, SG and Smith, A and Keenan, O and Barnhart, D and Zackular, JP},
title = {Comparison of Anaerobic Culture Methods for Detecting Clostridioides difficile in Bovine Faeces.},
journal = {Veterinary medicine and science},
volume = {11},
number = {1},
pages = {e70085},
doi = {10.1002/vms3.70085},
pmid = {39611384},
issn = {2053-1095},
support = {//Pennsylvania Department of Agriculture/ ; },
mesh = {Animals ; Cattle ; *Clostridioides difficile/isolation &amp; purification ; *Feces/microbiology ; *Cattle Diseases/microbiology/diagnosis/epidemiology ; Clostridium Infections/veterinary/diagnosis/microbiology/epidemiology ; Bacteriological Techniques/veterinary/methods ; Female ; },
abstract = {BACKGROUND: The study of the epidemiology of Clostridioides difficile in populations is greatly facilitated by the ability to isolate and further characterize individual organisms, which requires effective culture protocols. In cattle, where little is known about the epidemiology of C. difficile, no studies have assessed or compared the performance of different assays for detecting C. difficile.<br><br>OBJECTIVES: This study compared two culture protocols for detecting C. difficile in bovine faeces from 121 gestating cows and 70 of their neonatal calves, while situating results obtained with each protocol relative to those obtained with shotgun metagenomic sequencing.<br><br>METHODS: Protocol 1 involved direct plating enrichment onto taurocholine-cycloserine-cefoxitin-fructose agar (TCCFA), while Protocol 2 included an ethanol shock step before plating on CCFA/ChromID agar. For both protocols, one aliquot underwent broth enrichment prior to plating, while the other aliquot did not.<br><br>RESULTS: Clostridioides difficile was detected following broth enrichment in two of the same calf samples using both protocols, and an additional cow sample was found to be positive with Protocol 2, though the difference in detection rates was not statistically significant (p = 1.0).<br><br>CONCLUSIONS: The detection of C. difficile in a much high number of these samples by shotgun metagenomics, albeit at low levels of relative abundance, suggests that neither of these culture protocols is sensitive when levels of abundance are low.},
}
@article {pmid39611142,
year = {2024},
author = {Zhang, L and Zhang, H and Su, S and Jia, Y and Liang, C and Fang, Y and Hong, D and Li, T and Ma, F},
title = {Risk factor assessment and microbiome analysis in peritoneal dialysis-related peritonitis reveal etiological characteristics.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1443468},
pmid = {39611142},
issn = {1664-3224},
mesh = {Humans ; *Peritonitis/microbiology/etiology/diagnosis ; *Peritoneal Dialysis/adverse effects ; Male ; Female ; Middle Aged ; Risk Factors ; *Gastrointestinal Microbiome ; Aged ; Risk Assessment ; Adult ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Peritoneal dialysis-related peritonitis (PDRP) is one of the most common complications of peritoneal dialysis (PD). Understanding the risk factors and etiological characteristics is indispensable for infection prevention and improving the outcome and life quality.<br><br>METHODS: A total of 70 PD patients were separated into the PDRP group (n=25) and the control group (n=45). Variables, including gender, age, body mass index, primary diseases, and history of basic diseases, in the two groups were analyzed to assess the risk factors of PDRP. Metagenomic next-generation sequencing (mNGS) and microbial culture were compared in detecting pathogenic microorganisms. Gut microbiota analysis was performed in 35 PDRP patients based on mNGS data.<br><br>RESULTS: Dialysis time and times of dialysate change were the risk factors of PDRP, and times of dialysate change was the independent risk factor of PDRP (p = 0.046). mNGS produced higher sensitivity (65.79%) than microbial culture (36.84%) in identifying pathogenic microorganisms. Staphylococcus aureus and Klebsiella pneumoniae (four cases) were the most frequent pathogens causing PDRP, followed by Staphylococcus capitis (three cases). &#x3b2; diversity of the gut microbiota was significantly different between patients with fewer times of dialysate change (&#x2264;4) and more (>5), as well as between patients with gram-positive (G+) bacterial and gram-negative (G-) bacterial infection.<br><br>CONCLUSION: The dialysis time and times of dialysate changes not only are risk factors for peritonitis in PD patients but also stimulate significant changes in the gut microbiome structure in PDRP patients. These findings may provide a novel viewpoint for the management of patients with PDRP.},
}
@article {pmid39611100,
year = {2024},
author = {Ye, X and Lin, Y and Yang, J and Qi, B and Wei, X and Huang, Y and Wang, L},
title = {Deciphering the pathogen heterogeneity for precise diagnosis and personalized therapeutics of infections after kidney transplantation: insights from metagenomic next-generation sequencing.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1456407},
pmid = {39611100},
issn = {2235-2988},
mesh = {*Kidney Transplantation/adverse effects ; Humans ; *High-Throughput Nucleotide Sequencing ; *Precision Medicine/methods ; *Metagenomics/methods ; Male ; COVID-19/diagnosis/virology ; Female ; Middle Aged ; Adult ; SARS-CoV-2/genetics/isolation &amp; purification ; Sensitivity and Specificity ; Cytomegalovirus/genetics/isolation &amp; purification ; Pneumocystis carinii/genetics/isolation &amp; purification ; Cytomegalovirus Infections/diagnosis/virology/drug therapy ; },
abstract = {INTRODUCTION: The aim of this study was to compare the detection performance of mNGS against that of conventional tests (CT) in patients suffering from infection after kidney transplantation.<br><br>METHODS: A total of 138 samples from 85 kidney transplant patients with acute or chronic infections were simultaneously analyzed using mNGS and CT from July 2021 to August 2023.<br><br>RESULTS: Compared with CT, mNGS demonstrated a higher sensitivity (95.96% vs. 27.27%) but lower specificity (48.72% vs. 84.62%) in pathogen detection. Moreover, mNGS exhibited significant advantages in detecting mixed and rare infections. The pathogens commonly identified in kidney transplant patients were severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), followed by Pneumocystis jirovecii and Cytomegalovirus (CMV). mNGS guided the precise clinical diagnosis in 89.13% of cases and assisted in altering therapeutics from empirical antibiotic approaches to personalized plans in 56.10% of cases, including treatment escalation (40.65%), initiation (11.38%), drug adjustment (3.25%), and de-escalation (0.81%).<br><br>DISCUSSION: Our study demonstrated the superior detection performance of mNGS and its significant clinical value. This reflected the great potential of mNGS as a complementary clinical detection technology for kidney transplant patients.},
}
@article {pmid39611041,
year = {2024},
author = {Liu, L and Lian, ZH and Lv, AP and Salam, N and Zhang, JC and Li, MM and Sun, WM and Tan, S and Luo, ZH and Gao, L and Yuan, Y and Ming, YZ and OuYang, YT and Li, YX and Liu, ZT and Hu, CJ and Chen, Y and Hua, ZS and Shu, WS and Hedlund, BP and Li, WJ and Jiao, JY},
title = {Insights into chemoautotrophic traits of a prevalent bacterial phylum CSP1-3, herein Sysuimicrobiota.},
journal = {National science review},
volume = {11},
number = {11},
pages = {nwae378},
pmid = {39611041},
issn = {2053-714X},
abstract = {Candidate bacterial phylum CSP1-3 has not been cultivated and is poorly understood. Here, we analyzed 112 CSP1-3 metagenome-assembled genomes and showed they are likely facultative anaerobes, with 3 of 5 families encoding autotrophy through the reductive glycine pathway (RGP), Wood-Ljungdahl pathway (WLP) or Calvin-Benson-Bassham (CBB), with hydrogen or sulfide as electron donors. Chemoautotrophic enrichments from hot spring sediments and fluorescence in situ hybridization revealed enrichment of six CSP1-3 genera, and both transcribed genes and DNA-stable isotope probing were consistent with proposed chemoautotrophic metabolisms. Ancestral state reconstructions showed that the ancestors of phylum CSP1-3 may have been acetogens that were autotrophic via the RGP, whereas the WLP and CBB were acquired by horizontal gene transfer. Our results reveal that CSP1-3 is a widely distributed phylum with the potential to contribute to the cycling of carbon, sulfur and nitrogen. The name Sysuimicrobiota phy. nov. is proposed.},
}
@article {pmid39609930,
year = {2024},
author = {Paquette, AJ and Bhatnagar, S and Vadlamani, A and Gillis, T and Khot, V and Novotnik, B and De la Hoz Siegler, H and Strous, M and Rattray, JE},
title = {Ecology and biogeochemistry of the microbial underworld in two sister soda lakes.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {98},
pmid = {39609930},
issn = {2524-6372},
abstract = {BACKGROUND: Approximately 3.7 billion years ago, microbial life may have emerged in phosphate-rich salty ponds. Surprisingly, analogs of these environments are present in alkaline lake systems, recognized as highly productive biological ecosystems. In this study, we investigate the microbial ecology of two Canadian soda lake sediment systems characterized by naturally high phosphate levels.<br><br>RESULTS: Using a comprehensive approach involving geochemistry, metagenomics, and amplicon sequencing, we discovered that groundwater infiltration into Lake Goodenough sediments supported stratified layers of microbial metabolisms fueled by decaying mats. Effective degradation of microbial mats resulted in unexpectedly low net productivity. Evaporation of water from Last Chance Lake and its sediments led to saturation of brines and a habitat dominated by inorganic precipitation reactions, with low productivity, low organic matter turnover and little biological uptake of phosphorus, leading to high phosphate concentrations. Highly alkaline brines were found to be dominated by potentially dormant spore-forming bacteria. These saturated brines also hosted potential symbioses between Halobacteria and Nanoarchaeaota, as well as Lokiarchaea and bacterial sulfate reducers. Metagenome-assembled genomes of Nanoarchaeaota lacked strategies for coping with salty brines and were minimal for Lokiarchaea.<br><br>CONCLUSIONS: Our research highlights that modern analogs for origin-of-life conditions might be better represented by soda lakes with low phosphate concentrations. Thus, highly alkaline brine environments could be too extreme to support origin of life scenarios. These findings shed light on the complex interplay of microbial life in extreme environments and contribute to our understanding of early Earth environments.},
}
@article {pmid39609882,
year = {2024},
author = {Cloarec, LA and Bacchetta, T and Bruto, M and Leboulanger, C and Grossi, V and Brochier-Armanet, C and Flandrois, JP and Zurmely, A and Bernard, C and Troussellier, M and Agogué, H and Ader, M and Oger-Desfeux, C and Oger, PM and Vigneron, A and Hugoni, M},
title = {Lineage-dependent partitioning of activities in chemoclines defines Woesearchaeota ecotypes in an extreme aquatic ecosystem.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {249},
pmid = {39609882},
issn = {2049-2618},
mesh = {*Archaea/classification/genetics/metabolism ; *Lakes/microbiology ; *Phylogeny ; *Ecotype ; Ecosystem ; Metagenomics ; Microbiota ; Genome, Archaeal ; Water Microbiology ; Biodiversity ; },
abstract = {BACKGROUND: DPANN archaea, including Woesearchaeota, encompass a large fraction of the archaeal diversity, yet their genomic diversity, lifestyle, and role in natural microbiomes remain elusive. With an archaeal assemblage naturally enriched in Woesearchaeota and steep vertical geochemical gradients, Lake Dziani Dzaha (Mayotte) provides an ideal model to decipher their in-situ activity and ecology.<br><br>RESULTS: Using genome-resolved metagenomics and phylogenomics, we identified highly diversified Woesearchaeota populations and defined novel halophilic clades. Depth distribution of these populations in the water column showed an unusual double peak of abundance, located at two distinct chemoclines that are hotspots of microbial diversity in the water column. Genome-centric metatranscriptomics confirmed this vertical distribution and revealed a fermentative activity, with acetate and lactate as end products, and active cell-to-cell processes, supporting strong interactions with other community members at chemoclines. Our results also revealed distinct Woesearchaeota ecotypes, with different transcriptional patterns, contrasted lifestyles, and ecological strategies, depending on environmental/host conditions.<br><br>CONCLUSIONS: This work provides novel insights into Woesearchaeota in situ activity and metabolism, revealing invariant, bimodal, and adaptative lifestyles among halophilic Woesearchaeota. This challenges our precepts of an invariable host-dependent metabolism for all the members of this taxa and revises our understanding of their contributions to ecosystem functioning and microbiome assemblage. Video Abstract.},
}
@article {pmid39609754,
year = {2024},
author = {Wang, X and Li, H and Ma, L and Ren, J and Mahsa, F and Amin, AM and Zhao, J and Zhang, M and He, P},
title = {Toxoplasmosis in a case with multiple serous effusions and severe aplastic anemia.},
journal = {BMC infectious diseases},
volume = {24},
number = {1},
pages = {1361},
pmid = {39609754},
issn = {1471-2334},
support = {2023-XKCRC-06//Project of Clinical Research Center of Xi'an Jiaotong University/ ; 2022YFC2502700//National Key R&amp;D Program/ ; 2022YFC2502700//National Key R&amp;D Program/ ; },
mesh = {Humans ; *Anemia, Aplastic/complications ; Female ; Adult ; *Toxoplasma/genetics/isolation &amp; purification ; *Toxoplasmosis/complications/parasitology/diagnosis ; Immunocompromised Host ; Stem Cell Transplantation ; Tomography, X-Ray Computed ; High-Throughput Nucleotide Sequencing ; Pleural Effusion/parasitology ; },
abstract = {Toxoplasmosis, a parasitic disease, can cause fatal multi-organ failure in immunocompromised patients. The lack of specificity in the symptoms and the need to confirm a diagnosis of tachyzoites in fluids or tissues through microscopic examination leads to a delay in reaching a diagnosis. A 28-year-old woman with severe aplastic anemia received stem cell transplantation seven months ago, presented with fever. Computed Tomography scan and ultrasonography showed moderate pleural, pericardial, peritoneal, and pelvic effusions. Metagenomic next-generation sequencing of blood and alveolar lavage fluid was done, 11,082 and 17,154 sequence readings of Toxoplasma gondii were detected, accounting for 1.34% and 17.09% of genome coverage, respectively. Then, marrow aspirate smears showed Toxoplasma gondii tachyzoites and pseudocyst. This case report alerts clinicians about Toxoplasma gondii infection in stem cell transplantation patients with multiple serous effusions and fever. Clinical trial: Not applicable.},
}
@article {pmid39609616,
year = {2024},
author = {Kim, M and Parrish, RC and Tisza, MJ and Shah, VS and Tran, T and Ross, M and Cormier, J and Baig, A and Huang, CY and Brenner, L and Neuringer, I and Whiteson, K and Harris, JK and Willis, AD and Lai, PS},
title = {Host DNA depletion on frozen human respiratory samples enables successful metagenomic sequencing for microbiome studies.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1590},
pmid = {39609616},
issn = {2399-3642},
support = {R21 AI175965/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Metagenomics/methods ; *Microbiota/genetics ; *Sputum/microbiology ; *Cystic Fibrosis/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; Freezing ; Adult ; Cryopreservation ; Female ; High-Throughput Nucleotide Sequencing/methods ; Bacteria/genetics/isolation &amp; purification/classification ; Sequence Analysis, DNA/methods ; Male ; Respiratory System/microbiology ; },
abstract = {Most respiratory microbiome studies use amplicon sequencing due to high host DNA. Metagenomics sequencing offers finer taxonomic resolution, phage assessment, and functional characterization. We evaluated five host DNA depletion methods on frozen nasal swabs from healthy adults, sputum from people with cystic fibrosis (pwCF), and bronchoalveolar lavage (BAL) from critically ill patients. Median sequencing depth was 76.4 million reads per sample. Untreated nasal, sputum, and BAL had 94.1%, 99.2%, and 99.7% host reads, respectively. Host depletion effects varied by sample type, generally increasing microbial reads, species and functional richness; this was mediated by higher effective sequencing depth. Rarefaction curves showed species richness saturation at 0.5-2 million microbial reads. Most methods did not change Morisita-Horn dissimilarity for BAL and nasal samples although the proportion of gram-negative bacteria decreased for sputum from pwCF. Freezing did not affect the viability of Staphylococcus aureus but reduced the viability of Pseudomonas aeruginosa and Enterobacter spp.; this was mitigated by adding a cryoprotectant. QIAamp-based host depletion minimally impacted gram-negative viability even in non-cryoprotected frozen isolates. While some host depletion methods may shift microbial composition, metagenomics sequencing without host depletion severely underestimates microbial diversity of respiratory samples due to shallow effective sequencing depth and is not recommended.},
}
@article {pmid39608999,
year = {2024},
author = {Climacosa, FMM and Anlacan, VMM and Gordovez, FJA and Reyes, JCB and Tabios, IKB and Manalo, RVM and Cruz, JMC and Asis, JLB and Razal, RB and Abaca, MJM and Dacasin, AB and Espiritu, APN and Gapaz, NCLL and Lee Yu, MHL},
title = {Monitoring drug Efficacy through Multi-Omics Research initiative in Alzheimer's Disease (MEMORI-AD): A protocol for a multisite exploratory prospective cohort study on the drug response-related clinical, genetic, microbial and metabolomic signatures in Filipino patients with Alzheimer's disease.},
journal = {BMJ open},
volume = {14},
number = {11},
pages = {e078660},
doi = {10.1136/bmjopen-2023-078660},
pmid = {39608999},
issn = {2044-6055},
mesh = {Humans ; *Alzheimer Disease/drug therapy/genetics ; Philippines ; Prospective Studies ; Aged ; Cholinesterase Inhibitors/therapeutic use ; Rivastigmine/therapeutic use ; Donepezil/therapeutic use ; Cross-Sectional Studies ; Memantine/therapeutic use ; Male ; Female ; Metabolomics ; Gastrointestinal Microbiome/drug effects ; Multiomics ; },
abstract = {INTRODUCTION: Dementia is one of the leading causes of disability among older people aged 60 years and above, with majority eventually being diagnosed with Alzheimer's disease (AD). Pharmacological agents approved for dementia include acetylcholinesterase enzyme (AChE) inhibitors like rivastigmine, donepezil and galantamine and the N-methyl-D-aspartate (NMDA) receptor antagonist memantine, prescribed as monotherapy or in combination with each other, depending on the severity of disease. There is currently no available study demonstrating the clinical response to these drugs for AD in the Filipino population. Hence, this protocol aims to characterise the clinical, genetic, microbial and metabolic factors associated with drug responses to donepezil, rivastigmine and/or memantine for AD in a cohort of Filipinos with late-onset AD.<br><br>METHODS AND ANALYSIS: This protocol involves a multisite descriptive study that will use two study designs: (1) a descriptive, cross-sectional study to characterise the clinical profile of Filipino dementia patients with AD and (2) an exploratory prospective cohort study to investigate drug response-related genetic, gut microbiome and metabolome signatures of a subset of the recruited AD patients. At least 153 patients with mild or moderate AD aged 65 years old and above will be recruited regardless of their treatment status. A subset of these patients (n=60) who meet inclusion and exclusion criteria will be included further in the exploratory cohort study. These patients will be grouped according to their baseline medications and will be observed for treatment response in 6 months. The cognitive, functional and behavioural domains of patients and levels of functioning will be measured using different assessment tools. Drug responses of Filipino patients will then be investigated employing multi-omics technology to characterise genetic variations via whole exome sequencing, gut microbiome profile via shotgun metagenomic sequencing and metabolome profile via liquid chromatography with mass spectrometry.<br><br>ETHICS AND DISSEMINATION: The study has received ethical clearance from the Department of Health Single Joint Research Ethics Board (SJREB-2022-15). Results of psychometric scales will be made available to enrolled patients. The study results will be presented at national/international conferences and published in international peer-reviewed scientific journals, and summaries of the results will be provided to the study funders and institutional review boards of the three tertiary referral hospitals.<br><br>TRIAL REGISTRATION NUMBER: Philippine Health Research Registry ID PHRR230220-0054116; ClinicalTrials.gov ID NCT05801380.},
}
@article {pmid39608612,
year = {2024},
author = {Tinganelli, W and Puspitasari-Kokko, A and Sokol, O and Helm, A and Simoniello, P and Schuy, C and Lerchl, S and Eckert, D and Oppermann, J and Rehm, A and Janssen, S and Engel, D and Moeller, R and Romano, R and Horst, F and Boscolo, D and Fournier, C and Durante, M and Weber, U},
title = {FLASH Bragg-peak irradiation with a therapeutic carbon ion beam: first in vivo results.},
journal = {International journal of radiation oncology, biology, physics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijrobp.2024.11.089},
pmid = {39608612},
issn = {1879-355X},
abstract = {BACKGROUND AND PURPOSE: In recent years, ultra-high dose rate (UHDR) irradiation has emerged as a promising innovative approach to cancer treatment. Characteristic feature of this regimen, commonly referred to as FLASH effect, demonstrated primarily for electrons, photons or protons, is the improved normal tissue sparing, while the tumor control is similar to the one of the conventional dose-rate (CDR) treatments. The FLASH mechanism is, however, unknown. One major question is whether this effect is maintained when using densely ionizing (high-LET) heavy nuclei.<br><br>MATERIALS AND METHODS: Here we report the effects of 20 Gy UHDR heavy ion irradiation in clinically relevant conditions, i.e., at high-LET in the spread-out Bragg peak (SOBP) of a [12]C beam using an osteosarcoma mouse model.<br><br>RESULTS: We show that UHDR irradiation was less toxic in the normal tissue compared to CDR while maintaining tumor control. The immune activation was also comparable in UHDR and CDR groups. Both UHDR and CDR exposures steered the metagenome toward a balanced state.<br><br>CONCLUSIONS: These results suggest that the UHDR irradiations can improve the safety and effectiveness of heavy ion therapy, and provide a crucial benchmark for current mechanistic FLASH models. However, additional experiments are needed to validate these findings across other animal and tumor models.},
}
@article {pmid39608199,
year = {2024},
author = {Bhat, AH and Malik, IM and Tak, H and Ganai, BA and Bharti, P},
title = {Host, parasite, and microbiome interaction: Trichuris ovis and its effect on sheep gut microbiota.},
journal = {Veterinary parasitology},
volume = {333},
number = {},
pages = {110356},
doi = {10.1016/j.vetpar.2024.110356},
pmid = {39608199},
issn = {1873-2550},
abstract = {Sheep that are infected with gastrointestinal helminths experience a significant impact on their health and productivity. Among the helminths, nematodes like Haemonchus contortus, Oesophagostomum spp., Bunostomum trigonocephalum, Nematodirus battus, Trichostrongylus spp. and Teladorsagia circumcincta are particularly pathogenic. Understanding the interactions among parasites, hosts, and their microbiomes is crucial in developing new approaches in the management of parasites. This study examines the bacterial profile of Trichuris ovis, a highly prevalent nematode among Kashmir Merino sheep, and the influence of nematode infection on the caecal microbiome of its host. Sheep were selected based on T. ovis infection status, and samples were collected from infected and non-infected caecum. The 16S rRNA metagenomic analysis revealed distinct microbial communities in T. ovis, infected caecum, and non-infected caecum. Proteobacteria dominated the T. ovis microbiome, while infected caecum was rich in Bacteroidota and Spirochaetota, and non-infected caecum had a higher proportion of Firmicutes and Verrucomicrobiota. At the genus level, T. ovis was predominantly associated with Escherichia/Shigella, while infected caecum had higher proportions of Bacteroides, Prevotella, and Treponema. Non-infected caecum was characterized by WCHB1-41, Prevotella, and Succiniclasticum like genera. Alpha and beta diversity indicated significant differences in microbiome among the groups, with higher diversity observed in infected caecum. The study found T. ovis infection significantly alters the caecal microbiome of sheep, introducing potentially pathogenic bacteria and reducing beneficial ones. These findings underscore the complex relationship between host, parasite, and microbiome, highlighting the need for comprehensive strategies to manage helminth infections and their broader ecological impacts.},
}
@article {pmid39607975,
year = {2024},
author = {Abbasi, AM and Nasir, S and Bajwa, AA and Akbar, H and Ali, MM and Rashid, MI},
title = {A comparative study of the microbiomes of the ticks Rhipicephalus microplus and Hyalomma anatolicum.},
journal = {Parasite (Paris, France)},
volume = {31},
number = {},
pages = {74},
pmid = {39607975},
issn = {1776-1042},
support = {HEC-GCF-273//Higher Education Commission, Pakistan/ ; },
mesh = {Animals ; *Rhipicephalus/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Ixodidae/microbiology ; *Microbiota ; Pakistan ; Phylogeny ; Symbiosis ; Female ; Gastrointestinal Microbiome ; Coxiella/genetics/isolation &amp; purification/classification ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {Hyalomma anatolicum and Rhipicephalus microplus are tick species that are important vectors of numerous pathogens affecting both humans and livestock. Endosymbionts, such as Coxiella-like endosymbionts (CLE), Francisella-like endosymbionts (FLE), and Candidatus Midichloria, play a crucial role in the physiology and vector competence of these ticks. In this study, we investigated the microbial composition of H. anatolicum and R. microplus from four geographically distinct regions of Pakistan to assess whether environmental differences influence their microbiomes. We analyzed the ticks' gut microbiome targeting the V3-V4 hypervariable region of 16S rRNA for Illumina 16S metagenome NGS sequencing and processed overall 144 ticks. Analysis of gut bacterial composition resulted in observation of 1200 R. microplus and 968 H. anatolicum unique amplicon sequencing variants (ASVs). Relative abundance, Alpha diversity (Shannon, Faith's phylogenetic distance) and beta diversity metrics (Bray-Curtis, Jaccard and UniFrac) were analyzed and revealed that H. anatolicum ticks have significantly unique and diverse microbial communities with Acinetobacter indicus and Francisella-like endosymbionts dominating as opposed to Candidatus Midichloria. Rhipicephalus microplus exhibited results consistent with the previous studies with no major changes in microbiome including Coxiella-like endosymbionts as the major contributor. These findings suggest that geographical and environmental factors play a significant role in shaping the tick microbiome, with potential consequences for disease transmission and tick survivability. Further research is needed to elucidate the functional roles of these microbial shifts and their impact on public health and livestock in affected regions.},
}
@article {pmid39607585,
year = {2024},
author = {Huang, A and Marais, A and Zhang, Z and Candresse, T},
title = {Complete genome sequence of a new poacevirus infecting wild oat (Avena fatua L.) in France.},
journal = {Archives of virology},
volume = {169},
number = {12},
pages = {256},
pmid = {39607585},
issn = {1432-8798},
support = {China Scholarship Council//China Scholarship Council/ ; China Scholarship Council//China Scholarship Council/ ; },
mesh = {*Avena/virology ; *Genome, Viral/genetics ; *Plant Diseases/virology ; *Phylogeny ; France ; *Potyviridae/genetics/isolation &amp; purification/classification ; Whole Genome Sequencing ; High-Throughput Nucleotide Sequencing ; Viral Proteins/genetics ; RNA, Viral/genetics ; 3' Untranslated Regions/genetics ; },
abstract = {Using a high-throughput sequencing (HTS) approach, we report the discovery of a new poacevirus (family Potyviridae) in symptomatic wild oat (Avena fatua L.) plants collected near Bordeaux, France, in June 2023. A nearly complete genome sequence of 10,292 nucleotides (nt) was obtained. The genome encodes a large 3189-amino-acid (aa) polyprotein with all of the expected hallmarks of those of Potyviridae members. The 3' untranslated region (UTR) is 195 nt long, and the 5' UTR, whose sequence is likely missing a few terminal nucleotides despite repeated efforts at 5' RACE, is unusually long (531 nt), like that of triticum mosaic virus (TrMV). Pairwise sequence comparisons and phylogenetic analysis showed that the new virus is most closely related to TrMV and to Poaceae Liege poacevirus, a virus that was identified recently in Poaceae members in Belgium by metagenomics. The common name "wild oat poacevirus 1" (WOPV1) is proposed for this novel virus, which should be accommodated in a new species in the genus Poacevirus. Given that WOPV1 was identified in plants that were coinfected by several other viruses, no conclusions can be drawn at this stage about its potential pathogenicity.},
}
@article {pmid39606997,
year = {2024},
author = {Li, ZH and Zhang, Q and Wang, HF and Yu, TB and Wang, YL and Ma, JL and Yin, CQ and Shen, F and Xu, YD and Lian, XF and Wang, T},
title = {[Multicenter study on the detection of pathogens in primary infectious diseases of the spine using metagenomic next-generation sequencing technology].},
journal = {Zhonghua wai ke za zhi [Chinese journal of surgery]},
volume = {62},
number = {12},
pages = {1128-1135},
doi = {10.3760/cma.j.cn112139-20240715-00337},
pmid = {39606997},
issn = {0529-5815},
support = {21-1-4-rkjk-2-nsh//Qingdao City Science and Technology Benefiting the People Demonstration and Guidance Special Support Project/ ; 22-3-7-smjk-5-nsh//Qingdao City Science and Technology Benefiting the People Demonstration and Guidance Special Support Project/ ; },
abstract = {Objective: To explore the role of metagenomic next-generation sequencing (mNGS) in the diagnosis of pathogens in primary infectious diseases of the spine (IDS) and to reveal its pathogen spectrum. Methods: This is a retrospective case series study. Clinical data of 380 patients with primary IDS who were treated at four medical centers in China from December 2019 to April 2024 were retrospectively analyzed. Among them, 82 cases were from the Department of Spine Surgery at the Affiliated Hospital of Qingdao University, 129 cases were from the Orthopedics Section Ⅱ (Bone Infection), Public Health Clinical Center Affiliated to Shandong University, 112 cases were from the Department of Spine Surgery, Fuzhou Second General Hospital, and 57 cases were from the Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine. There were 238 males and 242 females, with an age of (61.4±13.1) years (range: 10 to 91 years). Specimens from the site of spinal infection were obtained for pathogen culture, pathological examination, and mNGS detection preoperatively or intraoperatively in all patients. The number, types, and positive rates of pathogens detected by the two methods were analyzed and compared using the Chi-square test. Results: Among the 380 patients, 320 had confirmed pathogenic bacteria, with the highest proportion being pyogenic bacterial infections, accounting for 76.9% (246/320). The most common pathogen was Staphylococcus aureus, accounting for 22.8% (73/320). Brucella accounted for 13.8% (44/320); Mycobacterium tuberculosis accounted for 6.3% (20/320). Fungal infections accounted for 3.4% (11/320), mainly Aspergillus and Candida. In addition, Mycoplasma was detected in 3 cases (0.9%) and Benacox body in 4 cases (1.2%). The pathogen spectrum constructed by mNGS covered 46 types of pathogens, higher than the 22 types detected by traditional methods. The positive rate of mNGS was 80.8% (308/381), significantly higher than the 27.9% (106/381) of traditional methods (χ[2]=182.53, P<0.01). Conclusions: mNGS improves the positive rate of pathogen diagnosis in IDS, detecting a broader spectrum of pathogens, and serves as a valuable complement to traditional diagnostic methods. Combining both methods in the diagnosis of IDS can maximize detection rates, providing robust evidence for precise anti-infective treatment.},
}
@article {pmid39606118,
year = {2024},
author = {Lin, L and Luo, L and Wu, M and Chen, J and Liao, Y and Zhang, H},
title = {Utilizing metagenomic next-generation sequencing and phylogenetic analysis to identify a rare pediatric case of Naegleria fowleri infection presenting with fulminant myocarditis.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1463822},
pmid = {39606118},
issn = {1664-302X},
abstract = {BACKGROUND: Naegleria fowleri (N. fowleri), a rare and typically lethal amoeba, most commonly causes primary amoebic meningoencephalitis (PAM). This case report describes an exceptionally rare presentation of fulminant myocarditis as the primary manifestation in a 6-year-old child, diverging from the typical neurological pathogenesis associated with N. fowleri infection. Beyond neurological afflictions, the child developed arrhythmias and cardiac failure, necessitating treatment with extracorporeal membrane oxygenation (ECMO).<br><br>METHODS: Diagnosis was confirmed via metagenomic next-generation sequencing (mNGS) of both blood and cerebrospinal fluid (CSF). This analysis not only substantiated the infection but also revealed a potential new genotype of N. fowleri, designated k39_3, suggesting broader genetic diversity than previously recognized.<br><br>RESULTS: Immediate treatment with Amphotericin B (Am B) and rifampin was initiated upon diagnosis. Despite aggressive management and supportive care, the patient failed to maintain hemodynamic stability, continued to show a decrease in cardiac output, and exhibited relentless progression of central nervous system failure, culminating in death within 72&#x2009;h.<br><br>CONCLUSION: Our report documents a rare pediatric case of N. fowleri infection presenting with fulminant myocarditis, revealing an unexpected clinical manifestation and broadening the known spectrum of its effects. This emphasizes the need for enhanced surveillance and targeted research to understand the pathogenic mechanisms and improve treatment strategies.},
}
@article {pmid39605913,
year = {2024},
author = {Chen, J and Ng, S and Xu, P and Chen, S and Li, S and Chen, X and Xie, L and Ge, J},
title = {Herbal formula xuling-jiangu improves bone metabolic balance in rats with ovariectomy-induced osteoporosis via the gut-bone axis.},
journal = {Frontiers in pharmacology},
volume = {15},
number = {},
pages = {1505231},
pmid = {39605913},
issn = {1663-9812},
abstract = {INTRODUCTION: The XuLing JianGu recipe (XLJGR) is an empirical traditional Chinese medicine formula used for the treatment of osteoporosis. This study aims to explore the effects of XLJGR on the intestinal microbiota composition and endogenous metabolites in ovariectomized (OVX) rats.<br><br>METHODS: An OVX rat model was established to evaluate the intervention effects of XLJGR. The measured indicators included bone density, serum bone metabolism markers, and an analysis of the types and abundances of intestinal microbiota, along with changes in endogenous metabolites. Additionally, MC3T3-E1 cells were used to validate the differential metabolites.<br><br>RESULTS: XLJGR significantly reduced the abundance of Bacteroides, Butyricicoccus, and other bacterial strains in the gut. KEGG metabolic pathway enrichment analysis showed that XLJGR intervention led to notable changes in pathways such as peptidoglycan biosynthesis, carbapenem biosynthesis, and vancomycin resistance. Moreover, XLJGR significantly upregulated key intestinal microbiota metabolites, including gabapentin(GAB), camphoric acid(CAA), and nonanedioic acid(AZA), thereby promoting the proliferation and osteogenic differentiation of MC3T3-E1 cells.<br><br>DISCUSSION: This study highlights the potential biomedical applications of XLJGR in promoting bone health by positively affecting intestinal microbiota and metabolic characteristics. These findings suggest that XLJGR may serve as a viable alternative in the treatment of osteoporosis, warranting further exploration of its therapeutic mechanisms and clinical applications.},
}
@article {pmid39605612,
year = {2024},
author = {Cumbo, F and Truglia, S and Weitschek, E and Blankenberg, D},
title = {Feature selection with vector-symbolic architectures: a case study on microbial profiles of shotgun metagenomic samples of colorectal cancer.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.18.624180},
pmid = {39605612},
issn = {2692-8205},
abstract = {UNLABELLED: The continuingly decreasing cost of next-generation sequencing has recently led to a significant increase in the number of microbiome-related studies, providing invaluable information for understanding host-microbiome interactions and their relation to diseases. A common approach in metagenomics consists of determining the composition of samples in terms of the amount and types of microbial species that populate them, with the goal to identify microbes whose profiles are able to differentiate samples under different conditions with advanced feature selection techniques. Here we propose a novel backward variable selection method based on the hyperdimensional computing paradigm, which takes inspiration from how the human brain works in the classification of concepts by encoding features into vectors in a high-dimensional space. We validated our method on public metagenomic samples collected from patients affected by colorectal cancer in a case/control scenario, by performing a comparative analysis with other state-of-the-art feature selection methods, obtaining promising results.<br><br>AUTHOR SUMMARY: Characterizing the microbial composition of metagenomic samples is crucial for identifying potential biomarkers that can distinguish between healthy and diseased states. However, the high dimensionality and complexity of metagenomic data present significant challenges in the context of accurately selecting features. Our backward variable selection method, based on the hyperdimensional computing paradigm, offers a promising approach to overcoming these challenges. By effectively reducing the feature space while preserving essential information, this method enhances the ability to detect critical microbial signatures associated with diseases like colorectal cancer, leading to more precise diagnostic tools.},
}
@article {pmid39605587,
year = {2024},
author = {Andermann, TM and Zeng, K and Guirales-Medrano, S and Groth, A and Ramachandran, BC and Sun, S and Sorgen, AA and Hill, L and Bush, AT and Liu, H and Jones, C and Roach, J and Conlon, BP and Rao, G and Chao, NJ and Fodor, AA and Sung, AD},
title = {The impact of transplant location on the gut microbiome and resistome in patients undergoing hematopoietic stem cell transplantation at home versus in the hospital.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.19.624359},
pmid = {39605587},
issn = {2692-8205},
abstract = {OBJECTIVES: Home-based hematopoietic stem cell transplantation (HCT) is a novel approach that has the potential to improve outcomes, however, the impact of transplant location on the gut microbiome remains uncharacterized. We hypothesized that patients randomized to undergo home HCT would have higher gut taxonomic diversity and lower antimicrobial resistance (AMR) gene abundance compared to those undergoing standard hospital HCT.<br><br>METHODS: We identified 28 patients enrolled in Phase II randomized trials of home (n=16) v. hospital (n=12) HCT at Duke and performed shotgun metagenomic sequencing of stools to compare taxonomic and AMR gene composition between groups. We performed a secondary analysis of patients from each group transplanted at an outpatient infusion clinic with those who underwent standard inpatient HCT ("outpatient" v. "inpatient").<br><br>RESULTS: No significant differences in duration of hospitalization were found in those randomized to home v. hospital HCT. Taxonomic and AMR gene &#x3b1;- and &#x3b2;-diversity were comparable. In contrast, secondary analyses demonstrated that patients from both home and hospital groups transplanted at an outpatient infusion clinic spent significantly less time in the hospital and demonstrated higher taxonomic &#x3b1;-diversity and differential &#x3b2;-diversity compared to standard inpatient HCT, although AMR gene &#x3b1;-diversity did not differ, and comparisons were confounded by both differences in transplant type and use of antibiotics.<br><br>CONCLUSIONS: Randomization by transplant location did not impact the gut microbiota to the same extent as the duration of hospitalization, although secondary analyses were heavily confounded. Even when taxonomic differences were observed, AMR genes were similar between groups.},
}
@article {pmid39605360,
year = {2024},
author = {Dai, Y and Qian, Y and Qu, Y and Guan, W and Xie, J and Wang, D and Butler, C and Dashper, S and Carroll, I and Divaris, K and Liu, Y and Wu, D},
title = {Longitudinal Microbiome-based Interpretable Machine Learning for Identification of Time-Varying Biomarkers in Early Prediction of Disease Outcomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.18.619118},
pmid = {39605360},
issn = {2692-8205},
abstract = {Information generated from longitudinally-sampled microbial data has the potential to illuminate important aspects of development and progression for many human conditions and diseases. Identifying microbial biomarkers and their time-varying effects can not only advance our understanding of pathogenetic mechanisms, but also facilitate early diagnosis and guide optimal timing of interventions. However, longitudinal predictive modeling of highly noisy and dynamic microbial data (e.g., metagenomics) poses analytical challenges. To overcome these challenges, we introduce a robust and interpretable machine-learning-based longitudinal microbiome analysis framework, LP-Micro, that encompasses: (i) longitudinal microbial feature screening via a polynomial group lasso, (ii) disease outcome prediction implemented via machine learning methods (e.g., XGBoost, deep neural networks), and (iii) interpretable association testing between time points, microbial features, and disease outcomes via permutation feature importance. We demonstrate in simulations that LP-Micro can not only identify incident disease-related microbiome taxa but also offers improved prediction accuracy compared to existing approaches. Applications of LP-Micro in two longitudinal microbiome studies with clinical outcomes of childhood dental disease and weight loss following bariatric surgery yield consistently high prediction accuracy. The identified critical early predictive time points are informative and aligned with clinical expectations.},
}
@article {pmid39604824,
year = {2024},
author = {Li, X and Zhang, Z and Bai, H and Liu, Z},
title = {Analysis of vaginal microbiota during postpartum and postmenopausal periods based on metagenomics.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {501},
pmid = {39604824},
issn = {1471-2180},
mesh = {Humans ; Female ; *Vagina/microbiology ; *Postmenopause ; *Postpartum Period ; *Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; Adult ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Postmenopausal and the postpartum periods are essential physiological phases that result in low estrogen levels in women; however, they are important to female reproductive health. Traditional as well as new detection methods (such as 16 S RNA sequencing) have limitations in detecting the composition of vaginal microbiota. Therefore, in this study, we used metagenomic detection technology to study the composition of vaginal microbiota in postmenopausal and postpartum women. Six women were randomly selected from each group (healthy women of childbearing age, postmenopausal group, and postpartum) for vaginal microecology, composition, α-diversity, linear discriminant analysis effect size (LEfSe), and Comprehensive Antibiotic Resistance Database (CARD) analyses.<br><br>RESULTS: We discovered that Lactobacillus dominance disappeared in postpartum and postmenopausal group women and that diversity increased. However, the proportions of Atopobium vaginae, Escherichia coli, and Streptococcus agalactiae significantly increased. Diversity was the highest in the postpartum period, with a significant increase in the proportions of A. vaginae, Gardnerella vaginalis, Prevotella, and occasionally, Chlamydia trachomatis. Linear discriminant analysis effect size analysis revealed that Lactobacillus crispatus and L. iners enrichment in the postpartum and menopausal periods was much lower than that in the childbearing age group. CARD analysis revealed that ABC-F ATP-binding cassette ribosomal protection protein subfamily gene abundance was significantly lower in the menopausal than in the childbearing age group, whereas the gimA family macrolide glycosyltransferase gene abundance was significantly higher.<br><br>CONCLUSIONS: The dominance of vaginal Lactobacillus in postpartum and menopausal women disappeared, while their diversity increased. In addition, the reproductive tract of postpartum women was susceptible to invasion by pathogenic microorganisms, which deserves clinical attention. When menopausal women receive treatment for vaginal infections, the likelihood that certain bacterial communities develop antibiotic resistance through ribosomal protection mechanisms is lower than that of women in the childbearing age, while the possibility of developing resistance to macrolides through glycosylation may increase. This, however, requires further research.},
}
@article {pmid39604809,
year = {2024},
author = {Li, Q and Wu, D and Song, Y and Zhang, L and Wang, T and Chen, X and Zhang, M},
title = {In vivo mechanism of the interaction between trimethylamine lyase expression and glycolytic pathways.},
journal = {Food &amp; function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo03809f},
pmid = {39604809},
issn = {2042-650X},
abstract = {Recent studies confirmed that host-gut microbiota interactions modulate disease-linked metabolite TMA production via TMA lyase. However, microbial enzyme production mechanisms remain unclear. In the present study, we investigated the impact of dietary and intervention factors on gut microbiota, microbial gene expression, and the interplay between TMA lyase and glycolytic pathways in mice. Using 16S rRNA gene sequencing, metagenomics, and metabolomics, the gut microbiota composition and microbial functional gene expression profiles related to TMA lyase and glycolytic enzymes were determined. The results revealed that distinct diets and intervention factors altered gut microbiota, gene expression, and metabolites linked to glycine metabolism and glycolysis. Notably, an arabinoxylan-rich diet suppressed genes linked to choline, glycine, glycolysis, and TMA lyase, favoring glycine utilization via pyruvate pathways. Glycolytic inhibitors amplified these effects, mainly inhibiting pyruvate kinase. Our findings underscored the crosstalk between TMA lyase and glycolytic pathways, regulating glycine levels, and suggested avenues for targeted interventions and personalized diets to curb choline TMA lyase production.},
}
@article {pmid39604726,
year = {2024},
author = {Chen-Liaw, A and Aggarwala, V and Mogno, I and Haifer, C and Li, Z and Eggers, J and Helmus, D and Hart, A and Wehkamp, J and Lamousé-Smith, ESN and Kerby, RL and Rey, FE and Colombel, JF and Kamm, MA and Olle, B and Norman, JM and Menon, R and Watson, AR and Crossett, E and Terveer, EM and Keller, JJ and Borody, TJ and Grinspan, A and Paramsothy, S and Kaakoush, NO and Dubinsky, MC and Faith, JJ},
title = {Gut microbiota strain richness is species specific and affects engraftment.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {39604726},
issn = {1476-4687},
abstract = {Despite the fundamental role of bacterial strain variation in gut microbiota function[1-6], the number of unique strains of a species that can stably colonize the human intestine is still unknown for almost all species. Here we determine the strain richness (SR) of common gut species using thousands of sequenced bacterial isolates with paired metagenomes. We show that SR varies across species, is transferable by faecal microbiota transplantation, and is uniquely low in the gut compared with soil and lake environments. Active therapeutic administration of supraphysiologic numbers of strains per species increases recipient SR, which then converges back to the population average after dosing is ceased. Stratifying engraftment outcomes by high or low SR shows that SR predicts microbial addition or replacement in faecal transplants. Together, these results indicate that properties of the gut ecosystem govern the number of strains of each species colonizing the gut and thereby influence strain addition and replacement in faecal microbiota transplantation and defined live biotherapeutic products.},
}
@article {pmid39604579,
year = {2024},
author = {Hao, Z and Lu, Y and Hao, Y and Luo, Y and Wu, K and Zhu, C and Shi, P and Zhu, F and Lin, Y and Zeng, X},
title = {Fungal mycobiome dysbiosis in choledocholithiasis concurrent with cholangitis.},
journal = {Journal of gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {39604579},
issn = {1435-5922},
support = {PWZxq2022-06//Key Disciplines Group Construction Project of Shanghai Pudong New Area Health Commission/ ; 82270636//National Natural Science Foundation of China/ ; 82070616//National Natural Science Foundation of China/ ; 82100608//National Natural Science Foundation of China/ ; PW2022D08//Joint Tackling Project of Pudong Health Committee of Shanghai/ ; PW2021A-38//Health and Family Planning Research Project of Pudong Health Committee of Shanghai/ ; PWYgf2021-02//Medical Discipline Construction Project of Pudong Health Committee of Shanghai/ ; 2022XD028//Talent Plan of the Shanghai Municipal Health Commission for Academic Leader/ ; },
abstract = {BACKGROUND: The gut mycobiome might have an important influence on the pathogenesis of choledocholithiasis concurrent with cholangitis (CC). The aim of this study was to characterize the fungal mycobiome profiles, explore the correlation and equilibrium of gut interkingdom network among bacteria-fungi-metabolites triangle in CCs.<br><br>METHODS: In a retrospective case-control study, we recruited patients with CC (n&#x2009;=&#x2009;25) and healthy controls (HCs) (n&#x2009;=&#x2009;25) respectively to analyze the gut fungal dysbiosis. Metagenomic sequencing was employed to characterize the gut mycobiome profiles, and liquid chromatography/mass spectrometry (LC/MS) analysis was used to quantify the metabolites composition.<br><br>RESULTS: The Shannon index displayed a reduction in fungal &#x3b1;-diversity in CCs compared to HCs (p&#x2009;=&#x2009;0.041), and the overall fungal composition differed significantly between two groups. The dominant 7 fungi species with the remarkable altered abundance were identified (LDA score&#x2009;>&#x2009;3.0, p&#x2009;<&#x2009;0.05), including CC-enriched Aspergillus_niger and CC-depleted fungi Saccharomyces_boulardii. In addition, the correlations between CC-related fungi and clinical variables in CCs were analyzed. Moreover, the increased abundance ratio of Basidiomycota-to-Ascomycota and a dense linkage of bacteria-fungi interkingdom network in CCs were demonstrated. Finally, we identified 30 markedly&#xa0;altered metabolites in CCs (VIP&#x2009;>&#x2009;1.0 and p&#x2009;<&#x2009;0.05), including low level of acetate and butyrate, and the deeper understanding on the complexity of bacteria-fungi-metabolites triangle involving bile inflammation was verified.<br><br>CONCLUSION: Our investigation demonstrated a distinct gut fungal dysbiosis in CCs and proposed that, beyond bacteria, the more attention should be paid to significantly potential influence of fungi and bacteria-fungi-metabolites triangle interkingdom interactions on pathogenesis of CC.},
}
@article {pmid39604411,
year = {2024},
author = {Purushothaman, S and Meola, M and Roloff, T and Rooney, AM and Egli, A},
title = {Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {29531},
pmid = {39604411},
issn = {2045-2322},
support = {310030_192512//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030_192512//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030_192512//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030_192512//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030_192512//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Metagenomics/methods ; *Nanopore Sequencing/methods ; *Drug Resistance, Bacterial/genetics ; DNA, Bacterial/genetics/isolation &amp; purification ; Humans ; Bacteria/genetics/isolation &amp; purification/classification ; },
abstract = {During a bacterial infection or colonization, the detection of antimicrobial resistance (AMR) is critical, but slow due to culture-based approaches for clinical and screening samples. Culture-based phenotypic AMR detection and confirmation require up to 72 hours (h) or even weeks for slow-growing bacteria. Direct shotgun metagenomics by long-read sequencing using Oxford Nanopore Technologies (ONT) may reduce the time for bacterial species and AMR gene identification. However, screening swabs for metagenomics is complex due to the range of Gram-negative and -positive bacteria, diverse AMR genes, and host DNA present in the samples. Therefore, DNA extraction is a critical initial step. We aimed to compare the performance of different DNA extraction protocols for ONT applications to reliably identify species and AMR genes using a shotgun long-read metagenomic approach. We included three different sample types: ZymoBIOMICS Microbial Community Standard, an in-house mock community of ESKAPE pathogens including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli (ESKAPE Mock), and anonymized clinical swab samples. We processed all sample types with four different DNA extraction kits utilizing different lysis (enzymatic vs. mechanical) and purification (spin-column vs. magnetic beads) methods. We used kits from Qiagen (QIAamp DNA Mini and QIAamp PowerFecal Pro DNA) and Promega (Maxwell RSC Cultured Cells and Maxwell RSC Buccal Swab DNA). After extraction, samples were subject to the Rapid Barcoding Kit (RBK004) for library preparation followed by sequencing on the GridION with R9.4.1 flow cells. The fast5 files were base called to fastq files using Guppy in High Accuracy (HAC) mode with the inbuilt MinKNOW software. Raw read quality was assessed using NanoPlot and human reads were removed using Minimap2 alignment against the Hg38 genome. Taxonomy identification was performed on the raw reads using Kraken2 and on assembled contigs using Minimap2. The AMR genes were identified using Minimap2 with alignment against the CARD database on both the raw reads and assembled contigs. We identified all bacterial species present in the Zymo Mock Community (8/8) and ESKAPE Mock (6/6) with Qiagen PowerFecal Pro DNA kit (chemical and mechanical lysis) at read and assembly levels. Enzymatic lysis retrieved fewer aligned bases for the Gram-positive species (Staphylococcus aureus and Enterococcus faecium) from the ESKAPE Mock on the assembly level compared to the mechanical lysis. We detected the AMR genes from Gram-negative and -positive species in the ESKAPE Mock with the QIAamp PowerFecal Pro DNA kit on reads level with a maximum median time of 1.9 h of sequencing. Long-read metagenomics with ONT may reduce the turnaround time in screening for AMR genes. Currently, the QIAamp PowerFecal Pro DNA kit (chemical and mechanical lysis) for DNA extraction along with the Rapid Barcoding Kit for the ONT sequencing captured the best taxonomy and AMR identification for our specific use case.},
}
@article {pmid39604397,
year = {2024},
author = {Carey-Ewend, K and Popkin-Hall, ZR and Simkin, A and Muller, M and Hennelly, C and He, W and Moser, KA and Gaither, C and Niaré, K and Aghakanian, F and Feleke, S and Brhane, BG and Phanzu, F and Kashamuka, MM and Aydemir, O and Sutherland, CJ and Ishengoma, DS and Ali, IM and Ngasala, B and Kalonji, A and Tshefu, A and Parr, JB and Bailey, JA and Juliano, JJ and Lin, JT},
title = {Population genomics of Plasmodium ovale species in sub-Saharan Africa.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {10297},
pmid = {39604397},
issn = {2041-1723},
support = {R21AI152260//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R21AI148579//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01AI65537//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; K24AI134990//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01AI129812//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01AI132547//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01TW010870//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; T32AI070114//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; },
mesh = {*Plasmodium ovale/genetics/classification/isolation &amp; purification ; Africa South of the Sahara/epidemiology ; Humans ; *Malaria/epidemiology/parasitology ; *Genome, Protozoan/genetics ; Genetic Variation ; Whole Genome Sequencing ; Tetrahydrofolate Dehydrogenase/genetics ; Phylogeny ; Merozoite Surface Protein 1/genetics ; Metagenomics ; Genomics/methods ; },
abstract = {Plasmodium ovale curtisi (Poc) and Plasmodium ovale wallikeri (Pow) are relapsing malaria parasites endemic to Africa and Asia that were previously thought to represent a single species. Amid increasing detection of ovale malaria in sub-Saharan Africa, we present a population genomic study of both species across the continent. We conducted whole-genome sequencing of 25 isolates from Central and East Africa and analyzed them alongside 20 previously published African genomes. Isolates are predominantly monoclonal (43/45), with their genetic similarity aligning with geography. Pow shows lower average nucleotide diversity (1.8×10[-4]) across the genome compared to Poc (3.0×10[-4]) (p < 0.0001). Signatures of selective sweeps involving the dihydrofolate reductase gene have been found in both species, as are signs of balancing selection at the merozoite surface protein 1 gene. Differences in the nucleotide diversity of Poc and Pow may reflect unique demographic history, even as similar selective forces facilitate their resilience to malaria control interventions.},
}
@article {pmid39604394,
year = {2024},
author = {Akiyama, S and Nishijima, S and Kojima, Y and Kimura, M and Ohsugi, M and Ueki, K and Mizokami, M and Hattori, M and Tsuchiya, K and Uemura, N and Kawai, T and Bork, P and Nagata, N},
title = {Multi-biome analysis identifies distinct gut microbial signatures and their crosstalk in ulcerative colitis and Crohn's disease.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {10291},
pmid = {39604394},
issn = {2041-1723},
mesh = {Humans ; *Colitis, Ulcerative/microbiology/genetics/virology ; *Crohn Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; Male ; *Metagenomics/methods ; Female ; *Bacteriophages/genetics ; Adult ; Escherichia coli/genetics/metabolism ; Middle Aged ; Japan ; Fungi/genetics ; Bacteria/genetics/metabolism/classification ; Metagenome/genetics ; Saccharomyces cerevisiae/genetics ; Bifidobacterium/genetics ; Virome/genetics ; Enterococcus faecium/genetics/pathogenicity ; Fatty Acids, Volatile/metabolism ; Young Adult ; China ; Case-Control Studies ; },
abstract = {The integrative multi-kingdom interaction of the gut microbiome in ulcerative colitis (UC) and Crohn's disease (CD) remains underinvestigated. Here, we perform shotgun metagenomic sequencing of feces from patients with UC and CD, and healthy controls in the Japanese 4D cohort, profiling bacterial taxa, gene functions, and antibacterial genes, bacteriophages, and fungi. External metagenomic datasets from the US, Spain, the Netherlands, and China were analyzed to validate our multi-biome findings. We found that Enterococcus faecium and Bifidobacterium spp. were enriched in both diseases. Enriched Escherichia coli was characteristic of CD and was linked to numerous antibiotic resistance genes involved in efflux pumps and adherent-invasive Escherichia coli virulence factors. Virome changes correlated with shifts in the bacteriome, including increased abundances of phages encoding pathogenic genes. Saccharomyces paradoxus and Saccharomyces cerevisiae were enriched in UC and CD, respectively. Saccharomyces cerevisiae and Escherichia coli had negative associations with short-chain fatty acid (SCFA)-producing bacteria in CD. Multi-biome signatures and their interactions in UC and CD showed high similarities between Japan and other countries. Since bacteria, phages, and fungi formed multiple hubs of intra- or trans-kingdom networks with SCFA producers and pathobionts in UC and CD, an approach targeting the interaction network may hold therapeutic promise.},
}
@article {pmid39603713,
year = {2024},
author = {Helfrich, PG and Feldman, J and Andrade-Barahona, E and Robertson, I and Foster, J and Hofacker, R and Dahlquist Selking, G and Sheik, CS and Cox, A},
title = {Aqueous copper geochemistry shapes the sediment microbial resistome in a recovering stream.},
journal = {Environmental microbiology reports},
volume = {16},
number = {6},
pages = {e70045},
doi = {10.1111/1758-2229.70045},
pmid = {39603713},
issn = {1758-2229},
support = {800015-10297//Montana Department of Justice, Natural Resource Damage Program (NRDP) through the Butte Natural Resource Damage Restoration Council (BNRC)/ ; //Montana Tech Faculty Seed and Faculty Development Initiatives/ ; //Montana Tech Earth Science and Engineering Fellowship/ ; //Montana Water Center, Faculty Seed Grant/ ; },
mesh = {*Copper/metabolism ; *Geologic Sediments/microbiology/chemistry ; *Rivers/microbiology/chemistry ; *Bacteria/genetics/drug effects/classification/metabolism/isolation &amp; purification ; Metagenome ; Water Pollutants, Chemical/metabolism ; Metagenomics ; Arsenic/metabolism ; Microbiota/genetics/drug effects ; },
abstract = {Aqueous metals are pervasive contaminants associated with historical mining. We produced and examined 16 metagenomes from a contaminated creek to investigate how anthropogenic metal contamination shapes the functional profiles of microbial communities. We then incorporated the metagenomic profiles and concurrently collected geochemical context into a multivariate model to examine correlations between stream geochemistry and microbial functional potential. Integrating the metagenomes with full geochemical profiles emphasised that even low metalloid concentrations shaped microbial functionality, seasonal shifts in copper bioavailability and arsenic exposure correlated with genetic variation, and copper resistomes were spatiotemporally distinct. This study provides new insights into microbial metabolic potential and microbe-metal(loid) interactions.},
}
@article {pmid39603479,
year = {2024},
author = {Guo, Q and Chen, X and Gong, H and Yang, J and Li, S and Zhu, D and Wang, X and Li, K and Zhang, Y and Zhou, S and Chen, K and Dai, X},
title = {Effect of inoculated sludge concentration on start-up of anammox reactor: Nitrogen removal performance and metabolic pathways.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131883},
doi = {10.1016/j.biortech.2024.131883},
pmid = {39603479},
issn = {1873-2976},
abstract = {The anammox process is efficient for nitrogen removal but faces challenges due to slow bacterial growth and limited inoculated sludge supply. This study examined the effects of different inoculated sludge concentrations (3.5, 7, and 14 g/L) on start-up and nitrogen metabolism in anammox reactors. Three identical reactors were operated under controlled conditions, with comprehensive analysis of nitrogen removal efficiency, sludge characteristics, and microbial community dynamics through metagenomic and transcriptomic approaches. Results demonstrated that higher inoculated sludge concentrations accelerated reactor start-up, with the 14 g/L reactor achieving stable operation in 13 days compared to 44 days for the 3.5 g/L reactor. However, the improvement in nitrogen removal rate showed a boundary effect, not proportional to the increase in sludge concentration. Notably, reactors with higher inoculated sludge concentrations exhibited lower sludge loads but higher sludge yield coefficients. Metagenomic analysis revealed Candidatus Kuenenia as the dominant anammox bacteria, with decreasing hydrazine dehydrogenase (hdh) gene expression levels observed at higher sludge concentrations, suggesting hydrazine synthesis as a potential rate-limiting step. This study provides novel insights into the optimal range of inoculated sludge concentration for anammox reactor start-up and elucidates the underlying metabolic mechanisms, offering valuable guidance for practical engineering applications.},
}
@article {pmid39603473,
year = {2024},
author = {Li, Y and Tao, C and Li, S and Chen, W and Fu, D and Jafvert, CT and Zhu, T},
title = {Feasibility study of machine learning to explore relationships between antimicrobial resistance and microbial community structure in global wastewater treatment plant sludges.},
journal = {Bioresource technology},
volume = {417},
number = {},
pages = {131878},
doi = {10.1016/j.biortech.2024.131878},
pmid = {39603473},
issn = {1873-2976},
abstract = {Wastewater sludges (WSs) are major reservoirs and emission sources of antibiotic resistance genes (ARGs) in cities. Identifying antimicrobial resistance (AMR) host bacteria in WSs is crucial for understanding AMR formation and mitigating biological and ecological risks. Here 24 sludge data from wastewater treatment plants in Jiangsu Province, China, and 1559 sludge data from genetic databases were analyzed to explore the relationship between 7 AMRs and bacterial distribution. The results of the Procrustes and Spearman correlation analysis were unsatisfactory, with p-value exceeding the threshold of 0.05 and no strong correlation (r > 0.8). In contrast, explainable machine learning (EML) using SHapley Additive exPlanation (SHAP) revealed Pseudomonadota as a major contributor (39.3 %-74.2 %) to sludge AMR. Overall, the application of ML is promising in analyzing AMR-bacteria relationships. Given the different applicable occasions and advantages of various analysis methods, using ML as one of the correlation analysis tools is strongly recommended.},
}
@article {pmid39603470,
year = {2024},
author = {Shang, Z and Zhang, X and Cheng, X and Li, S and Liang, X and Tao, Y and Sun, Y and Yu, Q and Li, Y},
title = {Impact of bioaugmentation on psychrophilic anaerobic digestion of corn straw.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131886},
doi = {10.1016/j.biortech.2024.131886},
pmid = {39603470},
issn = {1873-2976},
abstract = {In order to investigate the mechanisms by which bioaugmentation affects psychrophilic anaerobic digestion (AD), this study introduced a psychrophilic methanogenic culture into the sequencing batch of psychrophilic AD systems. The findings demonstrated that bioaugmentation boosted the abundance of Smithella (23.2 times), Syntrophobacter (9.9 times), and Methanothrix (1.4 times) in the psychrophilic AD systems, accelerating acetate and propionate degradation and improving methane production (26 %). Metagenomic analysis showed that bioaugmentation increased the relative abundance of genes related to propionate degradation and methane production, such as propionyl-CoA synthetase (45 %) and acetyl-CoA synthetase (11 %). At the cellular level, genes related to prevention of cell damage and promotion of membrane fluidity were upregulated. This study revealed the effect of bioaugmentation on microbial metabolic activities related to conversion of propionate to methane and cold tolerance in psychrophilic AD.},
}
@article {pmid39602961,
year = {2024},
author = {Cuevas-Ferrando, E and Sánchez, G and Pérez-Cataluña, A},
title = {Exploring plant virus diversity in wastewater and reclaimed water through metagenomic analysis.},
journal = {Water research},
volume = {270},
number = {},
pages = {122827},
doi = {10.1016/j.watres.2024.122827},
pmid = {39602961},
issn = {1879-2448},
abstract = {The use of reclaimed water for agricultural activities is being widely employed to address drought and water scarcity. Nevertheless, the disinfection processes do not consistently facilitate the complete removal of all eukaryotic viruses within these reclaimed waters. Consequently, it may pose a risk not only to humans but also to irrigated plants. We analyzed 48 influent and 48 effluent samples from 4 different wastewater treatment plants (WWTPs) by high-throughput sequencing (HTS) to characterize plant-associated virome over a one-year period. Our results showed high levels of plant viruses in both influent and effluent waters. The predominant family identified was Virgaviridae, recognized for its high environmental persistence. Notably, the identification of Tomato Brown Rugose Fruit virus (ToBRFV), classified as a harmful organism by the European Union and subject to strict containment measures to control its spread, highlights the importance of monitoring reclaimed water to mitigate the spread of such viruses into the environment. These findings underscore the need of analyzing reclaimed water from a One Health perspective, ensuring its safety for humans, animals, plants, and the environment alike.},
}
@article {pmid39602306,
year = {2024},
author = {Pasolli, E and Mauriello, IE and Avagliano, M and Cavaliere, S and De Filippis, F and Ercolini, D},
title = {Bifidobacteriaceae diversity in the human microbiome from a large-scale genome-wide analysis.},
journal = {Cell reports},
volume = {43},
number = {12},
pages = {115027},
doi = {10.1016/j.celrep.2024.115027},
pmid = {39602306},
issn = {2211-1247},
abstract = {We performed a large-scale genome-wide analysis aiming to investigate the prevalence and strain-level diversity of Bifidobacteriaceae species in the human microbiome. We considered 9,528 publicly available human metagenomes and integrated them with 1,192 isolate genomes from different sources. The prevalence and abundance of Bifidobacteriaceae species in humans was linked to multiple host characteristics: they were reduced in older people and enriched in populations characterized by Westernized lifestyles with geography-specific patterns. Phylogenetic analysis highlighted 110 Bifidobacteriaceae species-level genome bins (SGBs), with 32 found in humans and 8 in food and probiotic sources. Functional annotation revealed a great diversity in carbohydrate-active enzyme families across these SGBs. We found potential subspecies for most of the SGBs prevalent in humans and identified patterns driven by age and geography. We provided evidence that strains used in probiotics were rarely identified in humans, with the only exception represented by Bifidobacterium animalis. We finally evaluated that the abundance of Bifidobacteriaceae species exhibited moderate and variable capabilities to predict health status in case-control studies.},
}
@article {pmid39601988,
year = {2024},
author = {Rekadwad, BN and Shouche, YS and Jangid, K},
title = {Oil spill pollution and diversity analyses of resistant bacteria isolated from soil across the Arabian Sea and Bay of Bengal coastlines.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {12},
pages = {1265},
pmid = {39601988},
issn = {1573-2959},
mesh = {*Bacteria/classification/isolation &amp; purification/genetics ; *Petroleum Pollution ; *Environmental Monitoring ; India ; *Soil Microbiology ; Biodiversity ; Bays/microbiology ; Drug Resistance, Bacterial ; },
abstract = {Pelagic transport causes oil pollution via international tanker routes in the open ocean across southern Asia and the Indian Territory. Nutrient-rich runoff from residential, commercial, and industrial wastes, oil tanker mishaps, and sailing flags have all resulted in pollution. The natural flow of ocean water from east to west dragged pollutants into Indian Territory. We have investigated that the severe deposition of oil spills and biohazardous wastes is causing faunal mortality. Microbiome analyses helped us understand the sample's microbial load. 16S amplicon metagenome analysis, followed by enumeration and confirmation using molecular methods, indicates the presence of diverse microbial profiles. The presence of non-native hydrocarbon- and AMR-resistant bacterial taxa, such as Brevundimonas, Staphylococcus spp., Mycolicibacterium, Spingomonas spp., Bacillus spp., Chitinophaga spp., Priestia spp., Domibacillus spp., Rossellomorea spp., and Acinetobacter spp., confirms the impacts of oil and urban pollution. This indicates that the coastal soil of Goa and Andhra Pradesh has hydrocarbon- and antibiotic-resistant bacteria, which confirms that the present pollution status and that high-traffic recreational activities put biodiversity and humans at risk of getting illnesses linked to antibiotic resistance.},
}
@article {pmid39601762,
year = {2024},
author = {Fahy, JV and Jackson, ND and Sajuthi, SP and Pruesse, E and Moore, CM and Everman, JL and Rios, C and Tang, M and Gauthier, M and Wenzel, SE and Bleecker, ER and Castro, M and Comhair, SA and Erzurum, SC and Hastie, AT and Moore, W and Israel, E and Levy, BD and Denlinger, L and Jarjour, NN and Johansson, MW and Mauger, DT and Phillips, BR and Sumino, K and Woodruff, PG and Peters, MC and Seibold, MA and , },
title = {Type 1 Immune Responses Related to Viral Infection Influence Corticosteroid Response in Asthma.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1164/rccm.202402-0403OC},
pmid = {39601762},
issn = {1535-4970},
abstract = {RATIONALE: Corticosteroid-responsive type 2 (T2) inflammation underlies the T2-high asthma endotype. However, we hypothesized that type 1 (T1) inflammation, possibly related to viral infection, may also influence corticosteroid response.<br><br>OBJECTIVES: To determine the frequency and within-patient variability of T1-high, T2-high, and T1/T2-high asthma endotypes and whether virally influenced T1-high disease influences corticosteroid response in asthma.<br><br>METHODS: Patients in the Severe Asthma Research Program (SARP)-3 had sputum collected at baseline, after intramuscular (triamcinolone acetonide) corticosteroid treatment, and at 1 and 3-year follow-ups. Sputum cell RNA was used for whole transcriptome gene network and viral metagenomic analyses. We then profiled patients as highly expressing T1 and/or T2 gene networks and established the influence of these endotypes on corticosteroid responsiveness and likelihood of viral transcript detection in the airways.<br><br>MEASUREMENTS AND MAIN RESULTS: We found that 22% and 35% of asthma patients highly expressed T1 and T2 network genes, respectively, and that 8.5% highly expressed both networks. Asthma severity outcomes were worse in T2-high compared to T1-high asthma and most severe in the T1-high/T2-high subgroup. Corticosteroid treatment strongly suppressed T2 but poorly suppressed T1 gene expression, and corticosteroid-associated improvements in FEV1 occurred only in patients with T1-low/T2-high disease and not in T1-high/T2-high patients. Viral metagenomic analyses uncovered that 24% of asthma sputum samples tested positive for a respiratory virus and high viral carriage was associated with 14-fold increased risk of T1-high disease.<br><br>CONCLUSIONS: Airway type 1 immune responses are relatively common in asthma, are largely corticosteroid-resistant, and are associated with sub-clinical viral infection.},
}
@article {pmid39601584,
year = {2024},
author = {Chigwada, AD and Ogola, HJO and Tekere, M},
title = {A catalog of metagenomes and metagenome-assembled genomes from culture-enrichment microcosms containing polyethylene as carbon source.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0068924},
doi = {10.1128/mra.00689-24},
pmid = {39601584},
issn = {2576-098X},
abstract = {We present a data set detailing enrichment microbial consortia degrading polyethylene (PE) plastic. Derived from 180-day microcosm incubations using landfill soil, seawater, and cow dung, the data set includes three metagenomes and 23 metagenome-assembled genomes that capture microbial community interactions, structures, and functions relevant to PE biodegradation.},
}
@article {pmid39601556,
year = {2024},
author = {Yang, J and Wang, H and Lin, X and Liu, J and Feng, Y and Bai, Y and Liang, H and Hu, T and Wu, Z and Lai, J and Liu, J and Zou, Y and Wei, S and Yan, P},
title = {Gut microbiota dysbiosis induced by alcohol exposure in pubertal and adult mice.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0136624},
doi = {10.1128/msystems.01366-24},
pmid = {39601556},
issn = {2379-5077},
abstract = {UNLABELLED: Alcohol intake causes many diseases including neuropsychiatric symptoms, nutritional deficiency, progressive pancreatitis, liver cirrhosis, and ischemic heart disease. The gut microbiota changes significantly after alcohol exposure. Alcohol consumption tends to increase in underage and young people, but the feature of the gut microbiota in puberty remains largely unexplored. In this study, we conducted alcohol-exposed pubertal and adult mice model to investigate the intestinal damage and gut microbiota change. Interestingly, the responses of pubertal mice and adult mice after alcohol exposure were different. We found that alcohol dehydrogenase decreased and aldehyde dehydrogenase increased in the liver of pubertal mice, thus reducing the accumulation of toxic acetaldehyde. Furthermore, alcohol exposure caused less intestinal injury in pubertal mice. Through the analysis of metagenome assembly genome, we obtained many unrecognized bacterial genomes. Limosillactobacillus reuteri (cluster_56) and Lactobacillus intestinalis (cluster_57) were assembled from the samples of pubertal mice, which were involved in the production of indole acetic acid and the transformation of bile acids in response to alcohol exposure. This study provided a new insight to investigate the gut microbiota change and explained the difference of the gut microbiota after alcohol exposure between pubertal mice and adult mice.<br><br>IMPORTANCE: This study elucidates the significant impact of alcohol exposure on the gut microbiota and metabolic pathways in mice, highlighting the differential responses between adolescent and adult stages. Alcohol exposure was found to damage the intestinal barrier, alter the microbial composition by decreasing beneficial bacteria like Lactobacillus, and increase harmful bacteria such as Alistipes. The study also discovered unique microbial changes and resilience in pubertal mice. Species-level metagenomic analysis revealed specific microbial taxa and metabolic functions affected by alcohol. Metagenome-assembled genomes (MAGs) found many species that could not be annotated by conventional methods including many members of Lachnospiraceae, greatly expanding our understanding of the gut microbiota composition. These findings underscore the need for further research on alcohol's effects on various organs and the implications of microbial metabolites on disease progression.},
}
@article {pmid39601555,
year = {2024},
author = {Gao, Y and Zhang, H and Zhu, D and Guo, L},
title = {Different artificial feeding strategies shape the diverse gut microbial communities and functions with the potential risk of pathogen transmission to captive Asian small-clawed otters (Aonyx cinereus).},
journal = {mSystems},
volume = {},
number = {},
pages = {e0095424},
doi = {10.1128/msystems.00954-24},
pmid = {39601555},
issn = {2379-5077},
abstract = {UNLABELLED: Captive otters raised in zoos are fed different artificial diets, which may shape gut microbiota. The objective is to evaluate the impacts of two different artificial diets on microbial communities and function capabilities and short-chain fatty acid (SCFA) profiles in healthy otters' feces. A total of 16 Asian small-clawed otters in two groups (n = 8) were selected. Group A otters were fed raw loaches supplemented with commercial cat food (LSCF) diet, and group B otters were fed raw crucian diet. The communities and functional capabilities of microbiota in feces were assessed with metagenomic sequencing. Captive otters fed two kinds of diets possessed different gut microbial communities and functional capabilities. Various pathogenic bacteria, like Escherichia coli and Clostridium perfringens, were enriched in the samples from the two groups, respectively. Most of the differential pathways of nutrient metabolism were significantly enriched in group A, and the distributions of carbohydrate enzymes in the two groups significantly differed from each other. Multiple resistance genes markedly accumulated in fecal samples of the group A otters with LSCF diet. Higher concentrations of SCFAs were also observed in group A otters. Two feeding strategies were both likely to facilitate the colonization and expansion of various pathogenic bacteria and the accumulation of resistance genes in the intestines of captive otters, suggesting that risk of pathogen transmission existed in the current feeding process. Commercial cat food could supplement various nutrients and provide a substrate for the production of SCFAs, which might be beneficial for the otters' intestinal fermentation and metabolism.<br><br>IMPORTANCE: Captive otters fed with different diets possessed distinct gut microbial communities and functions, with the enrichment of several pathogens and multiple resistance genes in their gut microbiota. The current artificial feeding strategies had the possibility to accelerate the colonization and proliferation of various pathogenic bacteria in the intestines of otters and the spread of resistance genes, increasing the risk of diseases. In addition, supplementation with commercial cat food had benefits for otters' intestinal fermentation and the metabolism of gut microbiota.},
}
@article {pmid39601293,
year = {2024},
author = {Liu, L and Cao, S and Lin, W and Gao, Z and Yang, L and Zhu, L and Yang, B and Zhang, G and Zhu, R and Wu, D},
title = {miMatch: a microbial metabolic background matching tool for mitigating host confounding in metagenomics research.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2434029},
doi = {10.1080/19490976.2024.2434029},
pmid = {39601293},
issn = {1949-0984},
mesh = {*Metagenomics/methods ; Humans ; Gastrointestinal Microbiome ; Software ; Case-Control Studies ; Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Metagenome ; Propensity Score ; },
abstract = {Metagenomic research faces a persistent challenge due to the low concordance across studies. While matching host confounders can mitigate the impact of individual differences, the influence of factors such as genetics, environment, and lifestyle habits on microbial profiles makes it exceptionally challenging to create fully matched cohorts. The microbial metabolic background, which modulates microbial composition, reflects a cumulative impact of host confounders, serving as an ideal baseline for microbial sample matching. In this study, we introduced miMatch, an innovative metagenomic sample-matching tool that uses microbial metabolic background as a comprehensive reference for host-related variables and employs propensity score matching to build case-control pairs, even in the absence of host confounders. In the simulated datasets, miMatch effectively eliminated individual metabolic background differences, thereby enhancing the accuracy of identifying differential microbial patterns and reducing false positives. Moreover, in real metagenomic data, miMatch improved result consistency and model generalizability across cohorts of the same disease. A user-friendly web server (https://www.biosino.org/iMAC/mimatch) has been established to promote the integration of multiple metagenomic cohorts, strengthening causal relationships in metagenomic research.},
}
@article {pmid39600953,
year = {2024},
author = {Ma, T and Chu, J},
title = {Chemical structure metagenomics of microbial natural products: surveying nonribosomal peptides and beyond.},
journal = {Beilstein journal of organic chemistry},
volume = {20},
number = {},
pages = {3050-3060},
pmid = {39600953},
issn = {1860-5397},
abstract = {Bioactivity-guided fractionation (BGF) has historically been a fruitful natural product discovery workflow. However, it is plagued by increasing rediscovery rates in recent years and new methods capable of exploring the natural product chemical space more broadly and more efficiently is in urgent need. Chemical structure metagenomics as one such method is the theme of this Perspective. It emphasizes a chemical-structure-centered viewpoint toward natural product research. Key to chemical structure metagenomics is the ability to predict the structure of a natural product based on its biosynthetic gene sequences, which facilitated the discovery of numerous new bioactive molecules and helped uncover oversampled/underexplored niches of decades of BGF based discovery. While microbial nonribosomal peptides have been the focus of chemical structure metagenomics efforts thus far, it is in principle applicable to other natural product families. The future outlook of this new approach will also be discussed.},
}
@article {pmid39600931,
year = {2024},
author = {Pu, JF and Zhou, YL and Deng, M and Wu, J},
title = {Case report: A case of blood culture-negative Bartonella quintana endocarditis: blood mNGS is an efficient method for early diagnosis.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1449637},
pmid = {39600931},
issn = {2296-858X},
abstract = {Bartonella quintana is one of the main causes of blood culture-negative endocarditis, and routine blood culture and serological methods are difficult to achieve early diagnosis. We report a case of blood culture-negative Bartonella quintana endocarditis from southwestern Chongqing. The patient was a 67-year-old male scavenger who presented with heart failure without fever as the main clinical manifestation upon admission. He stated having had contact with stray cats in the past 2 months. The combination of clinical symptoms, echocardiography, and blood mNGS testing confirmed the infection of Bartonella quintana.},
}
@article {pmid39600877,
year = {2024},
author = {Cui, H and Ren, B and Wang, L and Chen, J and Li, J and Hu, W and Yang, Y},
title = {Enhanced pathogenicity and synergistic effects of co-infection with bovine viral diarrhea virus 1 and HoBi-like virus in cattle and guinea pigs.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1464745},
pmid = {39600877},
issn = {2297-1769},
abstract = {INTRODUCTION: The Bovine Viral Diarrhea Virus 1 (BVDV1) and HoBi-like virus (BVDV3), both within the same genus, share genomic homology and exhibit low antigenic cross-reactivity despite presenting similar clinical manifestations. In 2021, a bovine respiratory disease complex (BRDC) outbreak on two cattle farms in the Inner Mongolia Autonomous Region of China resulted in ten fatalities.<br><br>METHODS: Metagenomic and metatranscriptomic analyses were used to identify viral agents, including a co-infection case. A genetic evolution analysis assessed the relationships with related strains. Experimental infections in guinea pigs and calves evaluated the pathogenicity of the viruses.<br><br>RESULTS: Phylogenetic analysis of the BVDV3 isolate IM2201 revealed close relatedness to Brazilian strains, with 97.06% nucleotide homology to the highly virulent strain SV478/07. Experimental co-infection in guinea pigs resulted in more severe clinical signs, including fever, cough, diarrhea, and significant pathological changes, and led to a higher mortality rate (40%) compared to no mortality from single-virus infections with BVDV1 or BVDV3. Similarly, co-infected cattle exhibited more severe clinical signs, including bloody diarrhea and rectal temperatures exceeding 40&#xb0;C, along with persistent viremia and nasal viral shedding from 7 to 21 days post-infection. Blood analysis revealed significant reductions in white blood cell counts, particularly in co-infected cattle.<br><br>DISCUSSION: This study highlights the enhanced pathogenicity and synergistic effects of BVDV1 and BVDV3 co-infection, exacerbating disease severity.},
}
@article {pmid39600859,
year = {2024},
author = {Lin, HY and Tan, QH},
title = {Metagenomic next-generation sequencing may assist diagnosis of osteomyelitis caused by Mycobacterium houstonense: A case report.},
journal = {World journal of orthopedics},
volume = {15},
number = {11},
pages = {1095-1100},
pmid = {39600859},
issn = {2218-5836},
abstract = {BACKGROUND: Mycobacterium houstonense (M. houstonense) belongs to the nontuberculous mycobacterium group. Infection caused by M. houstonense is prone to recurrence.<br><br>CASE SUMMARY: We present a patient who was diagnosed with osteomyelitis caused by M. houstonense and treated with a combination of cefoxitin, and amikacin combined with linezolid.<br><br>CONCLUSION: The emergence of metagenomic next-generation sequencing (NGS) has brought new hope for the diagnosis and treatment of listeria meningitis. NGS can analyze a large number of nucleic acid sequences in a short time and quickly determine the pathogen species in the sample. Compared with traditional cerebrospinal fluid culture, NGS can greatly shorten the diagnosis time and provide strong support for the timely treatment of patients. Regarding treatment, NGS can also play an important role. Rapid and accurate diagnosis can enable patients to start targeted treatment as soon as possible and improve the treatment effect. At the same time, by monitoring the changes in pathogen resistance, the treatment plan can be adjusted in time to avoid treatment failure.},
}
@article {pmid39600479,
year = {2024},
author = {Xu, DZ and Tan, QH},
title = {Infection with Listeria monocytogenes meningoencephalitis: A case report.},
journal = {World journal of clinical cases},
volume = {12},
number = {33},
pages = {6629-6634},
pmid = {39600479},
issn = {2307-8960},
abstract = {BACKGROUND: Listeria meningitis is an infectious disease of the central nervous system caused by Listeria monocytogenes. This bacterium is widely present in the natural environment and can be transmitted through channels such as food and water. Patients usually show symptoms such as fever, headache, and neck stiffness. In severe cases, coma, convulsions, or even death may occur. Traditional diagnostic methods, such as cerebrospinal fluid (CSF) culture and serological tests, have certain limitations. Although CSF culture is the "gold standard" for diagnosis, it is time-consuming and has a relatively low positivity rate. Serological detection may also result in false positive or false negative results. The emergence of metagenomic sequencing (mNGS) technology has led to a significant breakthrough in diagnosing Listeria meningitis, allowing quick and accurate detection of various pathogens in samples.<br><br>CASE SUMMARY: Here, we present the case of a previously healthy 64-year-old woman diagnosed with Listeria meningitis using mNGS. She was successfully treated with intravenous ampicillin and meropenem, without any complications.<br><br>CONCLUSION: Listeria meningitis must be considered, especially in patients who fail to show improvement with first-line antibiotic treatments. mNGS significantly reduces the diagnosis time, supporting timely treatment of patients.},
}
@article {pmid39600212,
year = {2024},
author = {Zhao, H and Zhang, Z and Nair, S and Li, H and He, C and Shi, Q and Zheng, Q and Cai, R and Luo, G and Xie, S and Jiao, N and Zhang, Y},
title = {Overlooked Vital Role of Persistent Algae-Bacteria Interaction in Ocean Recalcitrant Carbon Sequestration and Its Response to Ocean Warming.},
journal = {Global change biology},
volume = {30},
number = {11},
pages = {e17570},
doi = {10.1111/gcb.17570},
pmid = {39600212},
issn = {1365-2486},
support = {tsqn202408283//Taishan Scholar Project of Shandong Province/ ; tsqn202312270//Taishan Scholar Project of Shandong Province/ ; QNESL OP202306//Qingdao New Energy Shandong Laboratory Open Project/ ; 42276105//National Natural Science Foundation of China/ ; 42476115//National Natural Science Foundation of China/ ; U1906216//National Natural Science Foundation of China/ ; //Ocean Negative Carbon Emissions (ONCE) program/ ; 2020YFA0607603//National Key Research and Development Program of China/ ; 2020YFA0608304//National Key Research and Development Program of China/ ; 2023YFE0113102//National Key Research and Development Program of China/ ; 2023220//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; },
mesh = {*Carbon Sequestration ; *Synechococcus/metabolism/growth &amp; development/physiology ; *Oceans and Seas ; *Seawater/microbiology/chemistry ; Carbon/metabolism ; Global Warming ; Bacteria/metabolism ; },
abstract = {Long-term carbon sequestration by the ocean's recalcitrant dissolved organic carbon (RDOC) pool regulates global climate. Algae and bacteria interactively underpin RDOC formation. However, on the long-term scales, the influence of their persistent interactions close to in situ state on ocean RDOC dynamics and accumulation remains unclear, limiting our understanding of the oceanic RDOC pool formation and future trends under global change. We show that a Synechococcus-bacteria interaction model system viable over 720 days gradually accumulated high DOC concentrations up to 84 mg L[-1]. Concurrently, the DOC inertness increased with the RDOC ratio reaching > 50%. The identified Synechococcus-bacteria-driven RDOC molecules shared similarity with over half of those from pelagic ocean DOC. Importantly, we provide direct genetic and metabolite evidence that alongside the continuous transformation of algal carbon by bacteria to generate RDOC, Synechococcus itself also directly synthesized and released RDOC molecules, representing a neglected RDOC source with ~0.2-1 Gt y[-1] in the ocean. However, we found that although ocean warming (+4°C) can promote algal and bacterial growth and DOC release, it destabilizes and reduces RDOC reservoirs, jeopardizing the ocean's carbon sequestration capacity. This study unveils the previously underestimated yet significant role of algae and long-term algae-bacteria interactions in ocean carbon sequestration and its vulnerability to ocean warming.},
}
@article {pmid39599910,
year = {2024},
author = {Queiroz-Ferreira, MS and Dos Reis, LNA and de Noronha Fonseca, ME and Melo, FFS and Reis, A and Boiteux, LS and Pereira-Carvalho, RC},
title = {Reexamination of the Sida Micrantha Mosaic Virus and Sida Mottle Virus Complexes: Classification Status, Diversity, Cognate DNA-B Components, and Host Spectrum.},
journal = {Viruses},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/v16111796},
pmid = {39599910},
issn = {1999-4915},
mesh = {*Begomovirus/genetics/classification/isolation &amp; purification ; *Phylogeny ; *Plant Diseases/virology ; *Genome, Viral ; *DNA, Viral/genetics ; Brazil ; Host Specificity ; Genetic Variation ; Malvaceae/virology ; Metagenomics/methods ; },
abstract = {Sida mottle virus (SiMoV) and Sida micrantha mosaic virus (SiMMV) are major Brazilian begomoviruses (Geminiviridae). However, the range of DNA-A identity of isolates of these viruses (81-100%) is not in agreement with the current criteria for Begomovirus species demarcation (<91%). To clarify this putative classification problem, we performed a comprehensive set of molecular analyses with all 53 publicly available isolates (with complete DNA-A genomes) designated as either SiMoV or SiMMV (including novel isolates obtained herein from nationwide metagenomics-based studies). Two well-defined phylogenetic clusters were identified. The SiMMV complex (n = 47) comprises a wide range of strains (with a continuum variation of 88.8-100% identity) infecting members of five botanical families (Malvaceae, Solanaceae, Fabaceae, Oxalidaceae, and Passifloraceae). The SiMoV group now comprises eight isolates (90-100% identity) restricted to Malvaceae hosts, including one former reference SiMMV isolate (gb|NC_077711) and SP77 (gb|FN557522; erroneously named as "true SiMMV"). Iteron analyses of metagenomics-derived information allowed for the discovery of the missing DNA-B cognate of SiMoV (93.5% intergenic region identity), confirming its bipartite nature. Henceforth, the correct identification of SiMoV and SiMMV isolates will be a crucial element for effective classical and biotech resistance breeding of the viral host species.},
}
@article {pmid39599892,
year = {2024},
author = {Gajurel, K and Dhakal, R and Deresinski, S},
title = {Arbovirus in Solid Organ Transplants: A Narrative Review of the Literature.},
journal = {Viruses},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/v16111778},
pmid = {39599892},
issn = {1999-4915},
mesh = {Humans ; *Arbovirus Infections/epidemiology/virology ; *Arboviruses ; *Organ Transplantation/adverse effects ; },
abstract = {The incidence of arbovirus infections has increased in recent decades. Other than dengue, chikungunya, and West Nile viruses, the data on arbovirus in solid organ transplant (SOT) are limited to case reports, and infections in renal transplant recipients account for most of the reported cases. Dengue and West Nile infections seem to be more severe with higher mortality in SOT patients than in the general population. Acute kidney injury is more frequent in patients with dengue and chikungunya although persistent arthralgia with the latter is less frequent. There is no clear relationship between arboviral infection and acute cellular rejection. Pre-transplant screening of donors should be implemented during increased arboviral activity but, despite donor screening and negative donor nucleic acid amplification test (NAT), donor derived infection can occur. NAT may be transiently positive. IgM tests lack specificity, and neutralizing antibody assays are more specific but not readily available. Other tests, such as immunohistochemistry, antigen tests, PCR, metagenomic assays, and viral culture, can also be performed. There are a few vaccines available against some arboviruses, but live vaccines should be avoided. Treatment is largely supportive. More data on arboviral infection in SOT are needed to understand its epidemiology and clinical course.},
}
@article {pmid39599783,
year = {2024},
author = {Vila-Nistal, M and Logares, R and Gasol, JM and Martinez-Garcia, M},
title = {Time Series Data Provide Insights into the Evolution and Abundance of One of the Most Abundant Viruses in the Marine Virosphere: The Uncultured Pelagiphages vSAG 37-F6.},
journal = {Viruses},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/v16111669},
pmid = {39599783},
issn = {1999-4915},
support = {PID2021-125175OB-I00//Agencia Estatal de Investigaci&#xf3;n/ ; CTM2015-70340-R//Agencia Estatal de Investigaci&#xf3;n/ ; RTI2018-101025-B-I00//Agencia Estatal de Investigaci&#xf3;n/ ; },
mesh = {*Seawater/virology ; *Metagenomics/methods ; Genome, Viral ; Phylogeny ; Evolution, Molecular ; Aquatic Organisms/virology ; Virome/genetics ; },
abstract = {Viruses play a pivotal role in ecosystems by influencing biochemical cycles and impacting the structure and evolution of their host cells. The widespread pelagiphages infect Pelagibacter spp., the most abundant marine microbe on Earth, and thus play a significant role in carbon transformation through the viral shunt. Among these viruses, the uncultured lytic pelagiphage vSAG 37-F6, uncovered by single-virus genomics, is likely the most numerous virus in the ocean. While previous research has delved into the diversity and spatial distribution of vSAG 37-F6, there is still a gap in understanding its temporal dynamics, hindering our insight into its ecological impact. We explored the temporal dynamics of vSAG 37-F6, assessing periodic fluctuations in abundance and evolutionary patterns using long- and short-term data series. In the long-term series (7 years), metagenomics showed negative selection acting on all viral genes, with a highly conserved overall diversity over time composed of a pool of yearly emergent, highly similar novel strains that exhibited a seasonal abundance pattern with two peaks during winter and fall and a decrease in months with higher UV radiation. Most non-synonymous polymorphisms occurred in structural viral proteins located in regions with low conformational restrictions, suggesting that many of the viral genes of this population are highly purified over its evolution. At the fine-scale resolution (24 h time series), combining digital PCR and metagenomics, we identified two peaks of cellular infection for the targeted vSAG 37-F6 viral strain (up to approximately 10[3] copies/ng of prokaryotic DNA), one before sunrise and the second shortly after midday. Considering the high number of co-occurring strains of this microdiverse virus, the abundance values at the species or genus level could be orders of magnitudes higher. These findings represent a significant advancement in understanding the dynamics of the potentially most abundant oceanic virus, providing valuable insights into ecologically relevant marine viruses.},
}
@article {pmid39599728,
year = {2024},
author = {Bedrač, L and Deutsch, L and Terzić, S and Červek, M and Šelb, J and Ašič, U and Verstraeten, LMG and Kuščer, E and Cvetko, F},
title = {Towards Precision Sports Nutrition for Endurance Athletes: A Scoping Review of Application of Omics and Wearables Technologies.},
journal = {Nutrients},
volume = {16},
number = {22},
pages = {},
doi = {10.3390/nu16223943},
pmid = {39599728},
issn = {2072-6643},
mesh = {Humans ; *Physical Endurance ; *Athletes ; *Wearable Electronic Devices ; *Sports Nutritional Physiological Phenomena ; Metabolomics/methods ; Precision Medicine/methods ; Biomarkers/blood ; Proteomics/methods ; Athletic Performance/physiology ; Nutrigenomics/methods ; Sports Nutritional Sciences ; Nutritional Status ; },
abstract = {BACKGROUND: Endurance athletes require tailored nutrition strategies to optimize performance, recovery, and training adaptations. While traditional sports nutrition guidelines provide a foundational framework, individual variability in metabolic responses underscores the need for precision nutrition, informed by genetic, biological, and environmental factors. This scoping review evaluates the application of systems biology-driven sports nutrition for endurance athletes, focusing on 'omics' and wearable technologies.<br><br>METHODS: A scoping review of the literature was conducted in PubMed, Scopus, and Web of Science in accordance with the PRISMA-ScR checklist. Research questions, search strategies, and eligibility criteria were guided by the Population-Concept-Context framework with the following inclusion criteria: original research in English, involving endurance athletes, systems biology approaches, and nutritional interventions or continuous glucose monitoring (CGM).<br><br>RESULTS: Fifty-two studies were included, with distance runners as the most studied cohort. Eleven studies used metagenomics, eleven CGM, ten nutrigenetics, ten metabolomics, seven multi-omics, one proteomics, one epigenomics, and one lipidomics. Over half (n = 31; 60%) were randomized controlled trials (RCTs) with generally high methodological quality.<br><br>CONCLUSIONS: Most studies were proof-of-concept investigations aimed at assessing biomarkers; however, the evidence linking these biomarkers to performance, recovery, and long-term health outcomes in endurance athletes remains insufficient. Future research should focus on well-powered replicated crossover RCTs, multivariate N-of-1 clinical trials, 360-degree systems-wide approaches, and the validation of genetic impacts on nutritional interventions to refine dietary guidelines.},
}
@article {pmid39599719,
year = {2024},
author = {Senaprom, S and Namjud, N and Ondee, T and Bumrungpert, A and Pongpirul, K},
title = {Sugar Composition of Thai Desserts and Their Impact on the Gut Microbiome in Healthy Volunteers: A Randomized Controlled Trial.},
journal = {Nutrients},
volume = {16},
number = {22},
pages = {},
doi = {10.3390/nu16223933},
pmid = {39599719},
issn = {2072-6643},
support = {FOODF67300006//Thailand Science Research and Innovation Fund Chulalongkorn University/ ; //The 90th Anniversary of Chulalongkorn University, Ratchadaphisek Somphot Fund/ ; //The Second Century Fund (C2F) for PhD Scholarship, Chulalongkorn University/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Adult ; Male ; Thailand ; Female ; Young Adult ; *Healthy Volunteers ; *Feces/microbiology ; Middle Aged ; Adolescent ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics ; Dietary Sugars ; Southeast Asian People ; },
abstract = {BACKGROUND: The relationship between consuming Thai desserts-predominantly composed of carbohydrates-and gut microbiome profiles remains unclear. This study aimed to evaluate the effects of consuming various Thai desserts with different GI values on the gut microbiomes of healthy volunteers.<br><br>METHODS: This open-label, parallel randomized clinical trial involved 30 healthy individuals aged 18 to 45 years. Participants were randomly assigned to one of three groups: Phetchaburi's Custard Cake (192 g, low-GI group, n = 10), Saraburi's Curry Puff (98 g, medium-GI group, n = 10), and Lampang's Crispy Rice Cracker (68 g, high-GI group, n = 10), each consumed alongside their standard breakfast. Fecal samples were collected at baseline and 24 h post-intervention for metagenomic analysis of gut microbiome profiles using 16S rRNA gene sequencing.<br><br>RESULTS: After 24 h, distinct trends in the relative abundance of various gut microbiota were observed among the dessert groups. In the high-GI dessert group, the abundance of Collinsella and Bifidobacterium decreased compared to the low- and medium-GI groups, while Roseburia and Ruminococcus showed slight increases. Correlation analysis revealed a significant negative relationship between sugar intake and Lactobacillus abundance in the medium- and high-GI groups, but not in the low-GI group. Additionally, a moderately negative association was observed between Akkermansia abundance and sugar intake in the high-GI group. These bacteria are implicated in energy metabolism and insulin regulation. LEfSe analysis identified Porphyromonadaceae and Porphyromonas as core microbiota in the low-GI group, whereas Klebsiella was enriched in the high-GI group, with no predominant bacteria identified in the medium-GI group.<br><br>CONCLUSIONS: The findings suggest that Thai desserts with varying GI levels can influence specific gut bacteria, though these effects may be temporary.},
}
@article {pmid39598209,
year = {2024},
author = {Al-Awthan, YS and Mir, R and Alharbi, BM and Alatawi, AS and Almutairi, FM and Khafaga, T and Shohdi, WM and Fakhry, AM and Alatawi, MM},
title = {Metagenomic Analysis of Sediment Bacterial Diversity and Composition in Natural Lakes and Artificial Waterpoints of Tabuk Region in King Salman Bin Abdulaziz Royal Natural Reserve, Saudi Arabia.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/life14111411},
pmid = {39598209},
issn = {2075-1729},
abstract = {The Tabuk region is located in the northern part of Saudi Arabia, and it has an area of 117,000 km[2] between longitudes 26° N and 29° N and latitudes 34° E and 38° E. King Salman Bin Abdulaziz Royal Natural Reserve (KSRNR) is the largest natural reserve in Saudi Arabia and covers about 130,700 km[2]. It represents a new tourist attraction area in the Tabuk region. Human activities around the lake may lead to changes in water quality, with subsequent changes in microenvironment components, including microbial diversity. The current study was designed to assess possible changes in bacterial communities of the water sediment at some natural lakes and artificial waterpoints of KSRNR. Water samples were collected from ten different locations within KSRNR: W1, W2, W3 (at the border of the royal reserve); W4, W5, W6, W7 (at the middle); and W8, W9, and W10 (artificial waterpoints). The total DNA of the samples was extracted and subjected to 16S rRNA sequencing and metagenomic analysis; also, the environmental parameters (temperature and humidity) were recorded for all locations. Metagenomic sequencing yielded a total of 24,696 operational taxonomic units (OTUs), which were subsequently annotated to 193 phyla, 215 classes, 445 orders, 947 families, and 3960 genera. At the phylum level, Pseudomonadota dominated the microbial communities across all samples. At the class level, Gammaproteobacteria, Clostridia, Alphaproteobacteria, Bacilli, and Betaproteobacteria were the most prevalent. The dominant families included Enterobacteriaceae, Pseudomonadaceae, Clostridiaceae, Comamonadaceae, and Moraxellaceae. At the genus level, Pseudomonas, Clostridium, Acinetobacter, Paenibacillus, and Acidovorax exhibited the highest relative abundances. The most abundant species were Hungatella xylanolytica, Pseudescherichia vulneris, Pseudorhizobium tarimense, Paenibacillus sp. Yn15, and Enterobacter sp. Sa187. The observed species richness revealed substantial heterogeneity across samples using species richness estimators, Chao1 and ACE, indicating particularly high diversity in samples W3, W5, and W6. Current study results help in recognizing the structure of bacterial communities at the Tubaiq area in relation to their surroundings for planning for environmental protection and future restoration of affected ecosystems. The findings highlight the dominance of various bacterial phyla, classes, families, and genera, with remarkable species richness in some areas. These results underscore the influence of human activities on microbial diversity, as well as the significance of monitoring and conserving the reserve's natural ecosystems.},
}
@article {pmid39598083,
year = {2024},
author = {Neiroukh, D and Hajdarpasic, A and Ayhan, C and Sultan, S and Soliman, O},
title = {Gut Microbial Taxonomy and Its Role as a Biomarker in Aortic Diseases: A Systematic Review and Future Perspectives.},
journal = {Journal of clinical medicine},
volume = {13},
number = {22},
pages = {},
doi = {10.3390/jcm13226938},
pmid = {39598083},
issn = {2077-0383},
abstract = {Background/Objectives: Evidence of the association between the gut microbiome and cardiovascular diseases has accumulated. An imbalance or dysbiosis of this system has been shown to play a role in the pathogenesis of cardiovascular events, including aortic diseases. We aimed to elucidate the findings of the gut microbial taxonomy associated with aortic diseases and their subtypes. Furthermore, we sought to investigate whether gut microbiome dysbiosis can be used as a biomarker for aortic disease detection and to identify which species can be disease-specific. Methods: A systematic search was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines for original research papers on gut microbiome composition in patients with aortic disease, using patients without aortic disease as the control (i.e., healthy controls). The databases PubMed, Scopus, Cochrane, and Web of Science were used by employing the medical subject headings (MeSH) terms "aortic diseases", "microbiome"," microbiota", and "taxa" before August 2024. We extracted the study characteristics, study population, and gut microbiome in aortic disease, including microbiota taxa diversity and abundance, regardless of taxa level. The National Institutes of Health (NIH) Quality Assessment Tool was used to assess study quality. Data were synthesized narratively to address the heterogeneity of the studies. Results: In this review, twelve studies that have identified gut microbial species and their potential impact on aortic disease pathogenesis were included. The studies showed the phyla dominance of Bacillota, Pseudomonadota, Actinomycetota, Bacteroidota, and Euryarchaeota in aortic disease patients. We also included the taxa sequencing methods and those used to extract the microorganisms. Aortic diseases were categorized into Takayasu's arteritis, giant cell arteritis, aortic aneurysm, and aortic dissection. Aortic disease patients had a higher rate of dysbiosis when compared to the healthy control groups, with significantly different microbiome composition. Conclusions: Patients with aortic disease exhibit a distinct difference between their gut microbiota composition and that of the healthy controls, which suggests a potential biomarker role of gut dysbiosis. Further exploration of the microbiome and its metagenome interface can help identify its role in aortic disease pathogenesis in depth, generating future therapeutic options. However, a unified methodology is required to identify potential microbial biomarkers in cardiovascular and cardiometabolic diseases.},
}
@article {pmid39597756,
year = {2024},
author = {Rosaldo-Benitez, V and Ayil-Chan, GA and Labrín-Sotomayor, N and Valdéz-Ojeda, R and Peña-Ramírez, YJ},
title = {Eukaryotic Microalgae Communities from Tropical Karstic Freshwater Lagoons in an Anthropic Disturbance Gradient Microscopic and Metagenomic Analysis.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112368},
pmid = {39597756},
issn = {2076-2607},
support = {5103711808//El Colegio de la Frontera Sur/ ; },
abstract = {The Yucatan aquifer sustains the people living in the Mayan forest and its associated fauna. Human activities threaten water quality and the environmental services associated with it. To assess the eukaryotic microalgae community structure as a bioindicator of water quality, we employed a combined approach of microscopic and shotgun metagenomics to identify specific genera associated with shifts in physicochemical parameters in three permanent lagoons located in Campeche, Mexico. We could identify highly complex and diverse communities independent of human activity intensity, harboring an average of 362 genera at each lagoon. Of those, 85 were affected by alkalinity, carbonates, water hardness, and cyanuric acid levels. Some genera, like Nannochloropsis and Thraustotheca, showed significant negative correlations with lead concentration. The functional annotation of genes revealed these communities' highly diverse metabolic capabilities and the pending work for extensive genomic characterization of rare clades.},
}
@article {pmid39597750,
year = {2024},
author = {Zell, R and Groth, M and Selinka, L and Selinka, HC},
title = {Metagenomic Analyses of Water Samples of Two Urban Freshwaters in Berlin, Germany, Reveal New Highly Diverse Invertebrate Viruses.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112361},
pmid = {39597750},
issn = {2076-2607},
abstract = {In an attempt to explore the RNA viromes of two German rivers, we searched the virus particle contents of one 50 L water sample each from the Teltow Canal and the Havel River for viruses assumed to infect invertebrates. More than 330 complete and partial virus genomes up to a length of 37 kb were identified, with noda-like and reo-like viruses being most abundant, followed by bunya-like and birna-like viruses. Viruses related to the Permutotetraviridae, Nidovirales, Flaviviridae, Rhabdoviridae and Chuviridae as well as the unclassified Jῑngmén virus and Negev virus groups were also present. The results indicate a broad extent of recombinant virus genomes, supporting the concept of the modularity of eukaryotic viruses. For example, novel combinations of genes encoding replicase and structural proteins with a jellyroll fold have been observed. Less than 35 viruses could be assigned to existing virus genera. These are (i) an avian deltacoronavirus which was represented by only one short contig, albeit with 98% similarity, (ii) a seadornavirus and a rotavirus, and (iii) some 30 nodaviruses. All remaining viruses are novel and too diverse for accommodation in existing genera. Many of the virus genomes exhibit ORFans encoding hypothetical proteins of up to 2000 amino acids without conserved protein domains.},
}
@article {pmid39597729,
year = {2024},
author = {Alexandrescu, L and Suceveanu, AP and Stanigut, AM and Tofolean, DE and Axelerad, AD and Iordache, IE and Herlo, A and Nelson Twakor, A and Nicoara, AD and Tocia, C and Dumitru, A and Dumitru, E and Condur, LM and Aftenie, CF and Tofolean, IT},
title = {Intestinal Insights: The Gut Microbiome's Role in Atherosclerotic Disease: A Narrative Review.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112341},
pmid = {39597729},
issn = {2076-2607},
abstract = {Recent advances have highlighted the gut microbiota as a significant contributor to the development and progression of atherosclerosis, which is an inflammatory cardiovascular disease (CVD) characterized by plaque buildup within arterial walls. The gut microbiota, consisting of a diverse collection of microorganisms, impacts the host's metabolism, immune responses, and lipid processing, all of which contribute to atherosclerosis. This review explores the complex mechanisms through which gut dysbiosis promotes atherogenesis. We emphasize the potential of integrating microbiota modulation with traditional cardiovascular care, offering a holistic approach to managing atherosclerosis. Important pathways involve the translocation of inflammatory microbial components, modulation of lipid metabolism through metabolites such as trimethylamine-N-oxide (TMAO), and the production of short-chain fatty acids (SCFAs) that influence vascular health. Studies reveal distinct microbial profiles in atherosclerosis patients, with increased pathogenic bacteria (Megamonas, Veillonella, Streptococcus) and reduced anti-inflammatory genera (Bifidobacterium, Roseburia), highlighting the potential of these profiles as biomarkers and therapeutic targets. Probiotics are live microorganisms that have health benefits on the host. Prebiotics are non-digestible dietary fibers that stimulate the growth and activity of beneficial gut bacteria. Interventions targeting microbiota, such as probiotics, prebiotics, dietary modifications, and faecal microbiota transplantation (FMT), present effective approaches for restoring microbial equilibrium and justifying cardiovascular risk. Future research should focus on longitudinal, multi-omics studies to clarify causal links and refine therapeutic applications.},
}
@article {pmid39597714,
year = {2024},
author = {Yang, T and He, Y and Yang, M and Gao, Z and Zhou, J and Wang, Y},
title = {Community Structure and Biodiversity of Active Microbes in the Deep South China Sea.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112325},
pmid = {39597714},
issn = {2076-2607},
support = {42376149//National Natural Science Foundation of China/ ; },
abstract = {The deep ocean harbors a group of highly diversified microbes, while our understanding of the active microbes that are real contributors to the nutrient cycle remains limited. In this study, we report eukaryotic and prokaryotic communities in ~590 m and 1130 m depths using 16S and 18S rRNA Illumina reads (miTags) extracted from 15 metagenomes (MG) and 14 metatranscriptomes (MT). The metagenomic 16S miTags revealed the dominance of Gammaproteobacteria, Alphaproteobacteria, and Nitrososphaeria, while the metatranscriptomic 16S miTags were highly occupied by Gammaproteobacteria, Acidimicrobiia, and SAR324. The consistency of the active taxa between the two depths suggests the homogeneity of the functional microbial groups across the two depths. The eukaryotic microbial communities revealed by the 18S miTags of the metagenomic data are dominated by Polycystinea; however, they were almost all absent in the 18S metatranscriptomic miTags. The active eukaryotes were represented by the Arthropoda class (at 590 m depth), Dinophyceae, and Ciliophora classes. Consistent eukaryotic communities were also exhibited by the 18S miTags of the metatranscriptomic data of the two depths. In terms of biodiversity, the ACE and Shannon indices of the 590 m depth calculated using the 18S metatranscriptomic miTags were much higher than those of the 1130 m depth, while a reverse trend was shown for the indices based on the metagenomic data. Our study reports the active microbiomes functioning in the nutrient utilization and carbon cycle in the deep-sea zone, casting light on the quantification of the ecological processes occurring in the deep ocean.},
}
@article {pmid39597671,
year = {2024},
author = {Skliros, D and Kostakou, M and Kokkari, C and Tsertou, MI and Pavloudi, C and Zafeiropoulos, H and Katharios, P and Flemetakis, E},
title = {Unveiling Emerging Opportunistic Fish Pathogens in Aquaculture: A Comprehensive Seasonal Study of Microbial Composition in Mediterranean Fish Hatcheries.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112281},
pmid = {39597671},
issn = {2076-2607},
support = {5010932//Operational Program Fisheries and Maritime 2014-2020/ ; },
abstract = {The importance of microbial communities in fish hatcheries for fish health and welfare has been recognized, with several studies mapping these communities during healthy rearing conditions and disease outbreaks. In this study, we analyzed the bacteriome of the live feeds, such as microalgae, rotifers, and Artemia, used in fish hatcheries that produce Mediterranean species. Our goal was to provide baseline information about their structure, emphasizing in environmental putative fish pathogenic bacteria. We conducted 16S rRNA amplicon Novaseq sequencing for our analysis, and we inferred 46,745 taxonomically annotated ASVs. Results showed that incoming environmental water plays a significant role in the presence of important taxa that constitute presumptive pathogens. Bio-statistical analyses revealed a relatively stable bacteriome among seasonal samplings for every hatchery but a diverse bacteriome between sampling stations and a distinct core bacteriome for each hatchery. Analysis of putative opportunistic fish pathogenic genera revealed some co-occurrence correlation events and a high average relative abundance of Vibrio, Tenacibaculum, and Photobacterium genera in live feeds, reaching a grand mean average of up to 7.3% for the hatchery of the Hellenic Center of Marine Research (HCMR), 12% for Hatchery A, and 11.5% for Hatchery B. Mapping the bacteriome in live feeds is pivotal for understanding the marine environment and distinct aquaculture practices and can guide improvements in hatchery management, enhancing fish health and sustainability in the Mediterranean region.},
}
@article {pmid39597660,
year = {2024},
author = {Rakitin, AL and Kulichevskaya, IS and Beletsky, AV and Mardanov, AV and Dedysh, SN and Ravin, NV},
title = {Verrucomicrobia of the Family Chthoniobacteraceae Participate in Xylan Degradation in Boreal Peat Soils.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112271},
pmid = {39597660},
issn = {2076-2607},
support = {075-15-2022-318//Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {The phylum Verrucomicrobiota is one of the main groups of soil prokaryotes, which remains poorly represented by cultivated organisms. The major recognized role of Verrucomicrobiota in soils is the degradation of plant-derived organic matter. These bacteria are particularly abundant in peatlands, where xylan-type hemicelluloses represent one of the most actively decomposed peat constituents. The aim of this work was to characterize the microorganisms capable of hydrolyzing xylan under the anoxic conditions typical of peatland soils. The laboratory incubation of peat samples with xylan resulted in the pronounced enrichment of several phylotypes affiliated with the Verrucomicrobiota, Firmicutes, and Alphaproteobacteria. Sequencing of the metagenome of the enrichment culture allowed us to recover high-quality metagenome-assembled genomes (MAGs) assigned to the genera Caproiciproducens, Clostridium, Bacillus (Firmicutes), and Rhizomicrobium (Alphaproteobacteria), Cellulomonas (Actinobacteriota) and the uncultured genus-level lineage of the family Chthoniobacteraceae (Verrucomicrobiota). The latter bacterium, designated "Candidatus Chthoniomicrobium xylanophilum" SH-KS-3, dominated in the metagenome and its MAG was assembled as a complete closed chromosome. An analysis of the SH-KS-3 genome revealed potential endo-1,4-beta-xylanases, as well as xylan beta-1,4-xylosidases and other enzymes involved in xylan utilization. A genome analysis revealed the absence of aerobic respiration and predicted chemoheterotrophic metabolism with the capacity to utilize various carbohydrates, including cellulose, and to perform fermentation or nitrate reduction. An analysis of other MAGs suggested that Clostridium and Rhizomicrobium could play the role of primary xylan degraders while other community members probably took advantage of the availability of xylo-oligosaccharides and xylose or utilized low molecular weight organics.},
}
@article {pmid39597632,
year = {2024},
author = {Köhler, JM and Ehrhardt, L and Günther, PM and Cao, J},
title = {Soil Bacteria in Archaeology: What Could Rank Abundance Functions Tell Us About Ancient Human Impacts on Microbial Communities?.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112243},
pmid = {39597632},
issn = {2076-2607},
support = {scholarship for L.E.//Th&#xfc;ringer Landesgraduiertenf&#xf6;rderung/ ; },
abstract = {Metagenomic analysis of soil bacterial communities based on 16S rRNA reflects a typical community composition containing a low number of high-abundance types and a very high number of low-abundance types. Here, the formation of characteristic rank order functions of bacterial abundance is investigated by modelling the dynamics of soil bacterial communities, assuming a succession of different bacterial populations that grow rapidly and decay more slowly. We found that the characteristic shape of typical rank order functions is well reflected by simulations. In addition, our model allowed us to investigate strong disturbances in the soil, which could be expected in cases of strongly changing local environmental conditions in soil, e.g., after translocation and covering of soil material. Such events could lead to the formation of shoulders in the rank order functions. Abundance rank orders observed in cases of some archaeological soil samples do indeed show such a shoulder and could be well interpreted by simulated rank order functions. As a result, it can be concluded that the investigations herein support our hypothesis that abundance rank orders contain information about the temporal order of developing bacterial types in changing communities and thus store information about local environmental conditions in the past, including ancient humans' impact on soil. This information can be used for interpretation of archeological findings and for reconstruction of different former human activities, as well as knowledge on the translocation of soil material in the past.},
}
@article {pmid39597631,
year = {2024},
author = {Li, Q and Wu, Y and Qi, X and Liu, Z and Wang, C and Ma, X and Ma, Y},
title = {Prickly Ash Seeds Improve the Ruminal Epithelial Development and Growth Performance of Hu Sheep by Modulating the Rumen Microbiota and Metabolome.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112242},
pmid = {39597631},
issn = {2076-2607},
support = {KJJC-LX-2023-05//Technology Integration Technology Project of Linxia Beef and Sheep Industry Development Re-search Institute/ ; 23JRRA1448//Science and Technology Plan Project of Gansu Province/ ; GAU-XKTD-2022-20//Discipline Team Project of Gansu Agricultural University/ ; },
abstract = {It is known that the addition of feed rich in bioactive components to animal diets will affect rumen fermentation parameters and flora structure. However, research on the regulatory effects of prickly ash seeds (PASs) during rumen development or on the rumen microbiome and its metabolites in sheep is limited. The current study was designed to explore the effects of PASs on sheep rumen development and growth performance using metagenomics and metabolomics. Eighteen 3-month-old Hu lambs were randomly allotted to three different dietary treatment groups: 0% (basal diet, CK), 3% (CK with 3% PAS, low-dose PAS, LPS), and 6% (CK with 6% PAS, high-dose PAS, HPS) PASs. The lambs were slaughtered to evaluate production performance. Our results showed that dietary PAS addition improved the average daily gain and reduced the F/G ratio of the experimental animals. Additionally, the height and width of the rumen papilla in the treatment groups were significantly higher than those in the CK group. The fermentation parameters showed that the levels of acetate and butyrate were significantly higher in the LPS group than in the CK and HPS groups. The propionate levels in the HPS group were significantly higher than those in the CK and LPS groups. Metagenomics analysis revealed that PAS dietary supplementation improved the abundance of Clostridiales and Bacteroidales and reduced the abundance of Prevotella, Butyrivibrio, and Methanococcus. Metabolomic analyses revealed that increased metabolite levels, such as those of serotonin, L-isoleucine, and L-valine, were closely related to growth-related metabolic pathways. The correlations analyzed showed that papilla height and muscular thickness were positively and negatively correlated with serotonin and L-valine, respectively. Average daily gain (ADG) was positively and negatively correlated with L-valine and several Prevotella, respectively. In addition, muscular thickness was positively correlated with Sodaliphilus pleomorphus, four Prevotella strains, Sarcina_sp_DSM_11001, and Methanobrevibacter_thaueri. Overall, PAS addition improved sheep growth performance by regulating beneficial microorganism and metabolite abundances, facilitating bacterial and viral invasion resistance.},
}
@article {pmid39597627,
year = {2024},
author = {Vilo, C and Fábrega, F and Campos, VL and Gómez-Silva, B},
title = {Microbial Biodiversity in Sediment from the Amuyo Ponds: Three Andean Hydrothermal Lagoons in Northern Chile.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112238},
pmid = {39597627},
issn = {2076-2607},
support = {FB 0001//ANID, Chile/ ; },
abstract = {The Amuyo Ponds (APs) are a group of three brackish hydrothermal lagoons located at 3700 m above sea level in a pre-Andean setting in the Atacama Desert. Each pond shows a conspicuous green (GP), red (RP), or yellow (YP) coloration, and discharges water rich in arsenic and boron into the Caritaya River (Camarones Basin, northern Chile). Microorganisms are subjected to harsh environmental conditions in these ponds, and the microbial composition and diversity in the Amuyo Ponds' sediments are unknown. The microbial life colonizing AP sediments was explored by metagenomics analyses, showing a diverse microbial life dominated by members of the bacterial domain, with nearly 800 bacterial genome sequences, and sequences associated with Archaea, Eukarya, and viruses. The genus Pseudomonas was more abundant in GP and YP sediments, while the genera Pseudomonas, Aeromonas, and Shewanella were enriched in RP sediments. Archaeal composition was similar in all sediments, and enriched with methanogens sequences from the Archaeoglobi and Halobacteria classes. Abundant fungi sequences were detected in all sediments from the phyla Blastocladiomycota and Ascomycota. We also report putative functional capabilities related to virulence and defense genes, the biosynthesis of secondary metabolites, and tolerance to arsenic. Thirteen bacterial and fourteen viral metagenome-assembled genomes were reconstructed and informed here. This work expands our knowledge on the richness of the microorganisms in the APs and open further studies on the ecology and genomics of this striking Andean geosite.},
}
@article {pmid39597611,
year = {2024},
author = {Lin, Q and Yang, P and Zhang, Y and Zhang, W and Wu, H},
title = {Metagenomic Insights into Coal Slag Remediation Effects on Soil and Microbial Health in Qinghai's Muli Coal Mine.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112222},
pmid = {39597611},
issn = {2076-2607},
support = {2021YFC3201604//Hongping Wu/ ; },
abstract = {Long-term coal mining in the Muli coal mine area of Qinghai Province has degraded soil quality and reduced microbial diversity, making it imperative to implement effective ecological restoration measures to restore soil quality and enhance ecosystem functions. This study evaluated soil samples under 11 ecological restoration treatments using metagenomic sequencing combined with soil quality analysis to explore the responses of the microbial community structure and function to identify effective restoration measures. This study demonstrated that ecological restoration significantly increased the soil microbial diversity and richness, with the MLII1 (soil samples treated with a chemical weathering agent, attapulgite, and a microbial agent) and MLIII1 (soil samples treated with sheep manure (2.4 kg/m[2]), granular organic fertilizer (1.2 kg/m[2]), and the microbial agent) treatment groups performing exceptionally well. Further analysis of the functional networks revealed that although the MLII2 (soil samples treated with the chemical weathering agent and attapulgite) treatment group did not exhibit the highest species diversity, it exhibited the highest functional network complexity. The results of hierarchical clustering analysis showed that the microbial community of the MLII2 treatment group was most similar to that of the natural meadows compared to the other treatment groups. From the perspective of overall ecological restoration, this study concluded that the MLII2 treatment group exhibited the most favorable ecological restoration outcomes. This finding emphasizes the importance of not only enhancing microbial diversity but also prioritizing the restoration of community functions, especially for the recovery of fragile high-altitude ecosystems.},
}
@article {pmid39597610,
year = {2024},
author = {Gáspár, Z and Nagavci, B and Szabó, BG and Lakatos, B},
title = {Gut Microbiome Alteration in HIV/AIDS and the Role of Antiretroviral Therapy-A Scoping Review.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112221},
pmid = {39597610},
issn = {2076-2607},
abstract = {(1) Background: The gut microbiota plays a crucial role in chronic immune activation associated with human immunodeficiency virus (HIV) infection, acquired immune deficiency syndrome (AIDS) pathogenesis, non-AIDS-related comorbidities, and mortality among people living with HIV (PLWH). The effects of antiretroviral therapy on the microbiome remain underexplored. This study aims to map the evidence of the impact of integrase strand transfer inhibitors (INSTI) and non-nucleoside reverse transcriptase inhibitors (NNRTI) on the gut microbiota of PLWH. (2) Methods: A scoping review was conducted using PubMed, Web of Science, and Embase, with reports collected following PRISMA for Scoping Reviews (PRISMA-ScR). (3) Results: Evidence suggests that INSTI-based regimes generally promote the restoration of alpha diversity, bringing it closer to that of seronegative controls, while beta diversity remains largely unchanged. INSTI-based therapies are suggested to be associated with improvements in microbiota composition and a tendency toward reduced inflammatory markers. In contrast, NNRTI-based treatments demonstrate limited recovery of alpha diversity and are linked to an increase in proinflammatory bacteria. (4) Conclusions: Based on the review of the current literature, it is indicated that INSTI-based antiretroviral therapy (ART) therapy facilitates better recovery of the gut microbiome.},
}
@article {pmid39597593,
year = {2024},
author = {Le Doujet, T and Haugen, P},
title = {The Microbiota of the Outer Gut Mucus Layer of the Migrating Northeast Arctic Cod (Gadus morhua) as Determined by Shotgun DNA Sequencing.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112204},
pmid = {39597593},
issn = {2076-2607},
support = {257146//ERA-MarineBiotech/ ; 000000//UiT The Arctic University of Norway/ ; },
abstract = {Animals form functional units with their microbial communities, termed metaorganisms. Despite extensive research on some model animals, microbial diversity in many species remains unexplored. Here, we describe the taxonomic profile of the microbes from the outer gut mucus layer from the Northeast Arctic cod using a shotgun DNA sequencing approach. We focused on the mucus to determine if its microbial composition differs from that of the fecal microbiota, which could reveal unique microbial interactions and functions. Metagenomes from six individuals were analyzed, revealing three different taxonomic profiles: Type I is dominated in numbers by Pseudomonadaceae (44%) and Xanthomonadaceae (13%), Type II by Vibrionaceae (65%), and Type III by Enterobacteriaceae (76%). This stands in sharp contrast to the bacterial diversity of the transient gut content (i.e., feces). Additionally, binning of assembled reads followed by phylogenomic analyses place a high-completeness bin of Type I within the Pseudomonas fluorescens group, Type II within the Photobacterium phosphoreum clade, and Type III within the Escherichia/Shigella group. In conclusion, we describe the adherent bacterial diversity in the Northeast Arctic cod's intestine using shotgun sequencing, revealing different taxonomic profiles compared to the more homogenous transient microbiota. This suggests that the intestine contains two separate and distinct microbial populations.},
}
@article {pmid39597583,
year = {2024},
author = {Wen, M and Liu, Y and Feng, C and Li, Z},
title = {Metagenomic Analysis Reveals the Effects of Different Land Use Types on Functional Soil Phosphorus Cycling: A Case Study of the Yellow River Alluvial Plain.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112194},
pmid = {39597583},
issn = {2076-2607},
support = {2019QZKK0501//the Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; },
abstract = {Phosphorus (P) is a crucial limiting nutrient in soil ecosystems, significantly influencing soil fertility and plant productivity. Soil microorganisms adapt to phosphorus deficiency and enhance soil phosphorus effectiveness through various mechanisms, which are notably influenced by land use practices. This study examined the impact of different land use types (long-term continuous maize farmland, abandoned evolving grassland, artificial tamarisk forests, artificial ash forests, and wetlands) on soil phosphorus-cycling functional genes within the Tanyang Forest Farm in a typical region of the Yellow River alluvial plain using macro genome sequencing technology. The gene cluster related to inorganic phosphorus solubilization and organic phosphorus mineralization exhibited the highest relative abundance across different land use types (2.24 × 10[-3]), followed by the gene cluster associated with phosphorus transport and uptake (1.42 × 10[-3]), with the lowest relative abundance observed for the P-starvation response regulation gene cluster (5.52 × 10[-4]). Significant differences were found in the physical and chemical properties of the soils and the relative abundance of phosphorus-cycling functional genes among various land use types. The lowest relative abundance of soil phosphorus-cycling functional genes was observed in forestland, with both forestland types showing significantly lower gene abundance compared to wetland, farmland, and grassland. Correlation analysis and redundancy analysis (RDA) revealed a significant relationship between soil physicochemical properties and soil phosphorus-cycling functional genes, with ammonium nitrogen, organic carbon, total nitrogen, and pH being the main environmental factors influencing the abundance of these genes, explaining 70% of the variation in their relative abundance. Our study reveals land use's impact on soil phosphorus-cycling genes, offering genetic insights into microbial responses to land use changes.},
}
@article {pmid39597569,
year = {2024},
author = {Miura, H and Tsukahara, T and Inoue, R},
title = {Whole-Genome Metagenomic Analysis of Functional Profiles in the Fecal Microbiome of Farmed Sows with Different Reproductive Performances.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112180},
pmid = {39597569},
issn = {2076-2607},
support = {23K14070//JSPS KAKENHI/ ; },
abstract = {Recent studies suggested an association between the reproductive performance of sows and their gut microbiota. To understand how the gut microbiota affect the reproductive performances of sows, we conducted a whole-genome metagenomic analysis on the fecal microbial functional profiles of sows with high and low reproductive performances. We used 60 sows from six farms (10 sows/farm), including 30 sows from three farms with higher reproductive performances (the mean number of weaned piglets/sow/year) (group H) and 30 sows from three farms with lower performances (group L). Fecal microbial DNA was subjected to a whole-genome metagenomic analysis. Biomarker exploration analysis identified "carbohydrate transport and metabolism" as the most discriminative function enriched in group H. Further analysis of carbohydrate-active enzymes revealed that the fecal microbiome of group H had a greater capacity to degrade dietary fiber, specifically cellulose and pectin. Group H also exhibited higher fecal short-chain fatty acid (SCFA) concentrations than group L, with the abundances of cellulose- and pectin-degrading genes showing significant positive correlations with fecal SCFA concentrations. Taxonomic analysis indicated greater contributions of Prevotella, Treponema, Ruminococcus, and Fibrobacter to cellulose and pectin degradation in the fecal microbiome in group H. In conclusion, higher reproductive performances of sows were, at least in part, associated with a greater microbial capacity for degrading cellulose and pectin, resulting in a higher SCFA production in the hindgut.},
}
@article {pmid39597568,
year = {2024},
author = {Jung, Y and Kim, I and Jung, DR and Ha, JH and Lee, EK and Kim, JM and Kim, JY and Jang, JH and Bae, JT and Shin, JH and Cho, YS},
title = {Aging-Induced Changes in Cutibacterium acnes and Their Effects on Skin Elasticity and Wrinkle Formation.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112179},
pmid = {39597568},
issn = {2076-2607},
support = {HP23C0061//Korea Health Industry Development Institute/Republic of Korea ; },
abstract = {Skin aging involves biomechanical changes like decreased elasticity, increased wrinkle formation, and altered barrier function. The skin microbiome significantly impacts this process. Here, we investigated the effects of decreased Cutibacterium acnes abundance and increase in other skin microorganisms on skin biomechanical properties in 60 healthy Koreans from Seoul, divided into younger (20-29 years) and older (60-75 years) groups. Metagenomic sequencing and skin assessments showed that the older group exhibited decreased C. acnes dominance and increased microbial diversity, correlating with reduced skin elasticity and increased wrinkles. In the younger age group, the enriched pathways included zeatin biosynthesis, distinct biotin metabolism pathways, and cofactor and vitamin metabolism in the younger age group, whereas pathways related to lipid metabolism, energy metabolism, and responses to environmental stressors, including UV damage and pollution, were enriched in the older group, according to functional analysis results. Network analysis indicated higher microbial connectivity in the younger group, suggesting a more stable community, whereas the older group's community displayed higher modularity, indicating more independent and specialized clusters. This study enhances our understanding of the impact of skin microbiome changes on skin aging, particularly the anti-aging effects of C. acnes. Future research should focus on the physiological mechanisms of skin microbiota on skin aging and explore therapeutic potentials to enhance skin health.},
}
@article {pmid39597565,
year = {2024},
author = {Liu, J and Zhou, L and Lan, Y and Fan, J},
title = {Breed Selection of Poplars Imposes Greater Selection Pressure on the Rhizosphere Bacterial Community.},
journal = {Microorganisms},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/microorganisms12112176},
pmid = {39597565},
issn = {2076-2607},
support = {2021YFD2201205 and 2021YFD2201203//National Key Research and Development Program of China/ ; },
abstract = {Breed selection alters the coevolution of plant-microbiome associations that have developed over long periods of natural evolution. We investigated the effects of breed selection on the rhizosphere microbiomes and metabolites of hybrid parents (I101 and 84K) and their offspring (Q1-Q5) using metagenomics and untargeted metabolomics. Rhizosphere archaeal, bacterial and fungal community β-diversity significantly differed among hybrid parents and offspring, but only the dominant bacterial phyla and bacterial community α-diversity revealed significant differences. Approximately 5.49%, 14.90% and 7.86% of the archaeal, bacterial and fungal species significantly differed among the poplar hybrid parents and offspring. Rhizosphere microbial functional genes and metabolites were both clustered into the following three groups: I101 and 84K; Q2 and Q4; and Q1, Q3 and Q5. Compared with the hybrid parents, 15 phytochemical compounds were enriched in the hybrid offspring and explained 7.15%, 18.24% and 6.68% of the total variation in the archaeal, bacterial and fungal community compositions, respectively. Rhizosphere metabolites significantly affected the bacterial community, rather than the archaeal and fungal communities. Our observations suggested that poplar breed selection imposed greater selection pressure on the rhizosphere bacterial community, which was mainly driven by metabolites.},
}
@article {pmid39596778,
year = {2024},
author = {Ulloa, F and Penati, M and Naegel, C and Tejeda, C and Hernández-Agudelo, M and Steuer, P and Salgado, M},
title = {Efficacy of Copper Ion Treatment on Bacteria and Antibiotic Residues Contained in Bovine Waste Milk.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/antibiotics13111085},
pmid = {39596778},
issn = {2079-6382},
support = {1240730//Fondecyt/ ; },
abstract = {Background/Objectives: Waste milk harbors many bacteria and antibiotic residues. Calves fed with untreated waste milk have a higher incidence of scours and an increased risk of developing antimicrobial-resistant bacteria. This study aimed to evaluate the efficacy of treatment with copper ions on bacteria and antibiotics contained in bovine waste milk. Methods: Waste milk samples were collected from a dairy farm for seven weeks and were subjected to treatment with copper ions. Total bacterial counts, coliforms, Streptococcus, and Staphylococcus were assessed before and after treatment. Additionally, metagenomic analysis was performed to determine microbial diversity. Results: Before treatment, the total bacterial count average was 4.0 × 10[6] CFU/mL, 1.7 × 10[4] CFU/mL for coliforms, 2.6 × 10[6] CFU/mL for Streptococcus, and 5.4 × 10[2] CFU/mL for Staphylococcus Copper treatment significantly reduced bacterial counts within 15 min. Total bacteria decreased from 4.0 × 10[6] CFU/mL to 1.1 × 10[2] CFU/mL after 30 min; meanwhile, other groups were not detected. The most abundant groups were Lactococcus (29.94%), Pseudomonas (28.89%), and Enterobacteriaceae (21.19%). Beta-lactams were detected in five-sevenths samples, and in one sample they were detected before and at 15 min of treatment but not after 30 min. Conclusions: The effect of treatment with copper ions on the different bacterial groups was significantly effective but showed limited effect on the detection of antibiotics.},
}
@article {pmid39596708,
year = {2024},
author = {Gyraitė, G and Kataržytė, M and Espinosa, RP and Kalvaitienė, G and Lastauskienė, E},
title = {Microbiome and Resistome Studies of the Lithuanian Baltic Sea Coast and the Curonian Lagoon Waters and Sediments.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/antibiotics13111013},
pmid = {39596708},
issn = {2079-6382},
support = {S-PD-22-80//Lietuvos Mokslo Taryba/ ; },
abstract = {BACKGROUND: the widespread use of antibiotics in human and veterinary medicine has contributed to the global challenge of antimicrobial resistance, posing significant environmental and public health risks.<br><br>OBJECTIVES: this study aimed to examine the microbiome and resistome dynamics across a salinity gradient, analyzing water and sediment samples from the Baltic Sea coast and the Curonian Lagoon between 2017 and 2023.<br><br>METHODS: the composition of the water and sediment bacterial community was determined by Full-Length Amplicon Metagenomics Sequencing, while ARG detection and quantification were performed using the SmartChipTM Real-Time PCR system.<br><br>RESULTS: the observed differences in bacterial community composition between the Baltic Sea coast and the Curonian Lagoon were driven by variations in salinity and chlorophyll a (chl a) concentration. The genera associated with infectious potential were observed in higher abundances in sediment than in water samples. Over 300 genes encoding antibiotic resistance (ARGs), such as aminoglycosides, beta-lactams, and multidrug resistance genes, were identified. Of particular interest were those ARGs that have previously been detected in pathogens and those currently classified as a potential future threat. Furthermore, our findings reveal a higher abundance and a distinct profile of ARGs in sediment samples from the lagoon compared to water.<br><br>CONCLUSIONS: these results suggest that transitional waters such as lagoons may serve as reservoirs for ARGs, and might be influenced by anthropogenic pressures and natural processes such as salinity fluctuation and nutrient cycling.},
}
@article {pmid39596705,
year = {2024},
author = {Moraes, BDGC and Martins, RCR and Fonseca, JVDS and Franco, LAM and Pereira, GCO and Bartelli, TF and Cortes, MF and Scaccia, N and Santos, CF and Musqueira, PT and Otuyama, LJ and Pylro, VS and Mariano, L and Rocha, V and Witkin, SS and Sabino, E and Guimaraes, T and Costa, SF},
title = {Impact of Exogenous Lactiplantibacillus plantarum on the Gut Microbiome of Hematopoietic Stem Cell Transplantation Patients Colonized by Multidrug-Resistant Bacteria: An Observational Study.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/antibiotics13111010},
pmid = {39596705},
issn = {2079-6382},
support = {FAPESP//001/ ; },
abstract = {Background:Lactiplantibacillus plantarum can inhibit the growth of multidrug-resistant organisms (MDROs) and modulate the gut microbiome. However, data on hematopoietic stem cell transplantation (HSCT) are scarce. Aim: In an observational study, we assessed the impact of L. plantarum on the modulation of the gut microbiome in HSCT patients colonized by MDROs. Methods: Participants were allocated to an intervention group (IG = 22) who received capsules of L. plantarum (5 × 10[9] CFU) twice per day until the onset of neutropenia or a control group (CG = 20). The V4 region of the 16S bacterial rRNA gene was sequenced in 87 stool samples from a subset of 33 patients (IG = 20 and CG = 13). The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) program was used to predict metagenome functions. Results:L. plantarum demonstrated an average 86% (±11%) drug-target engagement at 43 (±29) days of consumption and was deemed safe, well-tolerated, and associated with an increase in the abundance of the Lactobacillales (p < 0.05). A significant increase in Lactococcus and a reduction in Turicibacter (p < 0.05) were identified on the second week of L. plantarum use. Although Enterococcus abundance had a greater rise in the CG (p = 0.07), there were no significant differences concerning the Gram-negative MDROs. No serious adverse effects were reported in the IG. We observed a greater, non-significant pyruvate fermentation to propanoate I (p = 0.193) relative abundance in the IG compared with the CG. L. plantarum use was safe and tolerable by HSCT patients. Conclusions: While L. plantarum is safe and may impact Enterococcus and Turicibacter abundance, it showed no impact on Gram-negative MDRO abundance in HSCT patients.},
}
@article {pmid39596488,
year = {2024},
author = {Ali, S and Akhtar, MS and Siraj, M and Zaman, W},
title = {Molecular Communication of Microbial Plant Biostimulants in the Rhizosphere Under Abiotic Stress Conditions.},
journal = {International journal of molecular sciences},
volume = {25},
number = {22},
pages = {},
doi = {10.3390/ijms252212424},
pmid = {39596488},
issn = {1422-0067},
mesh = {*Rhizosphere ; *Stress, Physiological ; Plants/metabolism/microbiology ; Soil Microbiology ; Mycorrhizae/physiology/metabolism ; Plant Development ; Plant Growth Regulators/metabolism ; Bacteria/metabolism/genetics ; },
abstract = {Microbial plant biostimulants offer a promising, sustainable solution for enhancing plant growth and resilience, particularly under abiotic stress conditions such as drought, salinity, extreme temperatures, and heavy metal toxicity. These biostimulants, including plant growth-promoting rhizobacteria, mycorrhizal fungi, and nitrogen-fixing bacteria, enhance plant tolerance through mechanisms such as phytohormone production, nutrient solubilization, osmotic adjustment, and antioxidant enzyme activation. Advances in genomics, metagenomics, transcriptomics, and proteomics have significantly expanded our understanding of plant-microbe molecular communication in the rhizosphere, revealing mechanisms underlying these interactions that promote stress resilience. However, challenges such as inconsistent field performance, knowledge gaps in stress-related molecular signaling, and regulatory hurdles continue to limit broader biostimulant adoption. Despite these challenges, microbial biostimulants hold significant potential for advancing agricultural sustainability, particularly amid climate change-induced stresses. Future studies and innovation, including Clustered Regularly Interspaced Short Palindromic Repeats and other molecular editing tools, should optimize biostimulant formulations and their application for diverse agro-ecological systems. This review aims to underscore current advances, challenges, and future directions in the field, advocating for a multidisciplinary approach to fully harness the potential of biostimulants in modern agriculture.},
}
@article {pmid39596343,
year = {2024},
author = {Wang, Y and Wang, C and Hou, L and Yang, X and Li, C and Cui, S and Ma, C and Wang, L and Zhang, L and Liu, Y and Guo, H and Pan, J},
title = {Microbial Diversity and Biodegradation Mechanism of Microorganisms in the Dingtao M2 Tomb.},
journal = {International journal of molecular sciences},
volume = {25},
number = {22},
pages = {},
doi = {10.3390/ijms252212270},
pmid = {39596343},
issn = {1422-0067},
support = {Fundamental Research Funds for the Central Universities//University of Science and Technology Beijing/ ; },
mesh = {*Biodegradation, Environmental ; *Lignin/metabolism ; Wood/microbiology/metabolism ; Cellulose/metabolism ; China ; Talaromyces/metabolism/genetics ; Fungi/metabolism/genetics ; Peroxidases/metabolism ; Metagenomics/methods ; },
abstract = {The Dingtao M2 tomb, the largest and best-preserved imperial "Huangchangticou" tomb in China, holds great significance for its conservation. Currently, varying degrees of microbial degradation are occurring on the surfaces of the M2 tomb. This study aimed to determine the microbial diversity of the M2 tomb and its surrounding environment during July 2021 and August 2022. High-throughput metagenomic sequencing revealed that the dominant fungus on the surface of the tomb chamber was Dacrymyces stillatus (DTT1) in July 2021, which changed to Talaromyces pinophilus (DTT2) in August 2022. Enzymatic activities for cellulose and lignin degradation suggested that DTT1 has high levels of manganese peroxidase, lignin peroxidase, laccase, and cellulase. The wood of the tomb contained higher levels of Fe[2+] and Ca[2+], and experiments with different concentration gradients of these ions in the culture medium revealed that DTT1 exhibited greater activity of cellulose and lignin degradation in environments with higher concentrations of Fe[2+] and Ca[2+]. DTT2 degraded both cellulose and lignin. Lastly, a laboratory plate inhibition experiment demonstrated that isothiazolinone fungicide had a significant fungicidal effect on these two dominant fungi. This study provides valuable data and a theoretical basis for the preservation of the M2 tomb and other wooden cultural relics.},
}
@article {pmid39596262,
year = {2024},
author = {Mang, Q and Gao, J and Li, Q and Sun, Y and Xu, G and Xu, P},
title = {Probiotics Enhance Coilia nasus Growth Performance and Nutritional Value by Regulating Glucolipid Metabolism via the Gut-Liver Axis.},
journal = {International journal of molecular sciences},
volume = {25},
number = {22},
pages = {},
doi = {10.3390/ijms252212196},
pmid = {39596262},
issn = {1422-0067},
support = {32302976//National Natural Science Foundation of China/ ; BK20230179//Natural Science Foundation of Jiangsu Province/ ; 2022YFD2400904//National Key Research and development Program of China/ ; JSGS[2021]134//Jiangsu Province seed industry revitalization "revealing-list" project/ ; },
mesh = {*Probiotics/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Liver/metabolism ; Nutritive Value ; Lipid Metabolism ; Fishes/metabolism/growth &amp; development ; Animal Feed ; Glycolipids/metabolism ; },
abstract = {Large-scale intensive feeding triggered reduced growth performance and nutritional value. Exogenous probiotics can promote the growth performance and nutritional value of fish through improving the intestinal microbiota. However, detailed research on the correlation between the intestinal microbiota, growth performance, and nutritional value remains to be elucidated. Therefore, we performed metagenomic and metabolomic analysis to investigate the effects of probiotic addition to basal diet (1.0 × 10[8] CFU/g) (PF) and water (1.0 × 10[8] CFU/g) (PW) on the growth performance, muscle nutritional value, intestinal microbiota and their metabolites, and glucolipid metabolism in Coilia nasus. The results showed that FBW, BL, and SGR were enhanced in PF and PW groups. The concentrations of EAAs, TAAs, SFAs, MUFAs, and PUFAs were increased in PF and PW groups. Metagenomic and metabolic analyses revealed that bacterial community structure and metabolism were changed in the PF and PW groups. Moreover, adding probiotics to diet and water increased SCFAs and bile acids in the intestine. The gene expression associated with lipolysis and oxidation (hsl, pparα, cpt1, and acadm) and glycolysis (gck and pfk) was upregulated, while the gene expression associated with lipid synthesis (srebp1, acc, dgat, and elovl6) and gluconeogenesis (g6pca1, g6pca2, and pck) was downregulated in the liver. Correlation analysis displayed that hepatic glucolipid metabolism was regulated through the microbiota-gut-liver axis. Mantel test analysis showed that growth performance and muscle nutritional value were improved by the gut-liver axis. Our findings offered novel insights into the mechanisms that underlie the enhancement of growth performance and nutritional value in C. nasus and other fish by adding probiotics.},
}
@article {pmid39595367,
year = {2024},
author = {Pellegrini, F and Lanave, G and Caringella, F and Diakoudi, G and Salvaggiulo, A and Cavalli, A and Papaleo, A and Di Martino, B and Camero, M and Bányai, K and Matthijnssens, J and Martella, V},
title = {Identification of Recombinant Aichivirus D in Cattle, Italy.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/ani14223315},
pmid = {39595367},
issn = {2076-2615},
support = {. PE00000007, INF-ACT//Ministero dell'Universit&#xe0; e della ricerca Piano Nazionale di Ripresa e Resilienza MUR PNRR Ex-tended Partnership initiative on Emerging Infectious Diseases/ ; National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, RRF-2.3.1-21-2022-00001//National Research, Development and Innovation Office, Hungary/ ; RRF-2.3.1-21-2022-00010 (National Laboratory of Virology)//National Research, Development and Innovation Office, Hungary/ ; },
abstract = {Kobuviruses (KoVs) are a group of small, non-enveloped RNA viruses classified in the genus Kobuvirus within the Picornaviridae family, comprising Aichivirus species A to F. KoVs have been identified in humans and several mammals, including domestic ungulates. This study investigated the presence of KoVs in a collection of bovine stool samples (n = 38) obtained from animals with enteritis or without clinical signs. By RT-PCR screening, KoV RNA was detected in 10/38 animals (26.3%). Six of the ten positive animals had enteric signs. On sequence analysis of the amplicons, eight strains were related to species Aichivirus B, commonly identified in cattle. In contrast, two strains (ITA/2019/572-1 and ITA/2020/bovine/30-2), displayed the highest nt identity (up to 97.1%) to cattle, yak, and goat Aichivirus D strains. On whole genome analysis, strains ITA/2019/572-1 and ITA/2020/30-2 showed 88.9% nt identity to each other and 87.8-90.3% nt to the bovine kobuvirus strain CHN/2021/ON730709 identified in China. Interestingly these three Aichivirus D strains showed a recombinant makeup, clustering with D1 genotype in the capsid region and with D2 genotype in the non-structural genes. These findings suggest that Aichivirus D KoVs are common components of livestock virome. Understanding the genetic diversity of KoVs in animals will be useful to improve the diagnostics and gather epidemiological data.},
}
@article {pmid39595278,
year = {2024},
author = {Zeng, Y and Mou, H and He, Y and Zhang, D and Pan, X and Zhou, L and Shen, Y and E, G},
title = {Effects of Key Rumen Bacteria and Microbial Metabolites on Fatty Acid Deposition in Goat Muscle.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/ani14223225},
pmid = {39595278},
issn = {2076-2615},
support = {32272834&#xff1b;32360813//National Natural Science Foundation of China/ ; SWU-XDJH202301//Fundamental Research Funds for the Central Universities/ ; },
abstract = {In this study, the fatty acid composition in the muscles of Hechuan white goats was correlated with the metabolome and metagenome of their rumen contents, and potential effects of the metabolites and microorganisms in the rumen on host muscle fatty acid deposition were analyzed. The results of the correlation analysis between the rumen content's metabolome and muscle fatty acid content showed that vitamin-B-related metabolites were significantly correlated with fatty acid content (p < 0.05). Most of these metabolites were positively correlated with stearic acid and negatively correlated with palmitic acid. In accordance with the level of fatty acid content, significant differences were found in the microbial species and abundance among groups at the species level. An abundance of Bacteroides, Ruminococcaceae P7, Eubacterium ruminant, and Prevotella in the rumen was significantly correlated with fatty acid content. These results provide data support for the development of targeted feeding management strategies to improve the quality of goat meat.},
}
@article {pmid39595275,
year = {2024},
author = {Thomson, P and Garrido, D and Santibáñez, R and Lara, F},
title = {Preliminary Functional Analysis of the Gut Microbiome in Colic Horses.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/ani14223222},
pmid = {39595275},
issn = {2076-2615},
support = {11231174//ANID. FONDECYT Iniciaci&#xf3;n/ ; },
abstract = {The gut microbiome plays a critical role in maintaining horse health, influencing digestion, immunity, and overall well-being. However, in certain conditions like colic, there is evidence of significant alterations in the microbial community. To analyze the composition of the fecal microbiome and the enriched predicted metabolic functions of horses with colic compared to a control group, 14 horses with colic and 14 control horses were recruited. From a stool sample, DNA extraction was carried out for subsequent 16S rRNA metagenomic analysis. The composition of the microbiome was analyzed from the sequences of each sample using the QIIME version 1.8.0 and DADA2 version 1.22 programs. PICRUSt2 was used to predict metabolic functions. Statistical analyses were performed with the Mann-Whitney U test from the Python scipy v1 package. The gut microbiomes of both groups were dominated by Firmicuteota, Bacteroidota, and Pseudomonadota phyla. Colic in horses was associated with reduced diversity, reduced abundance of Fibrobacter, and an increase in Streptococcus. The abundance of Firmicuteota was negatively correlated with Pseudomonadota and Actinobacteriota. The equine colic microbiome was predicted to be enriched in aerobic respiration pathways and fatty acid and amino acid degradation. These observations indicate discrete but important differences in the gut microbiome of colic horses.},
}
@article {pmid39595245,
year = {2024},
author = {Yu, M and Li, Z and Cui, Y and Rong, T and Tian, Z and Deng, D and Liu, Z and Zhang, R and Ma, X},
title = {An Integrated Profiling of Liver Metabolome and Transcriptome of Pigs Fed Diets with Different Starch Sources.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/ani14223192},
pmid = {39595245},
issn = {2076-2615},
support = {32372928//National Natural Science Foundation of China/ ; 2024A1515030187//Guangdong Basic and Applied Basic Research Foundation/ ; },
abstract = {Diets containing higher-amylose-content starches were proved to have some beneficial effects on monogastric animals, such as promoting the proliferation of intestinal probiotics. However, current research on the effects of diets with different starch sources on animals at the extraintestinal level is still very limited. We hypothesized that diets with different starch sources may affect lipid-related gene expression and metabolism in the liver of pigs. This study aimed to use adult pig models to evaluate the effects of diets with different starch sources (tapioca starch, TS; pea starch, PS) on the liver gene expressions and metabolism. In total, 48 growing pigs were randomly assigned to the TS and PS diets with 8 replicate pens/group and 3 pigs per pen. On day 44 of the experiment, liver samples were collected for metabolome and transcriptome analysis. Metabolome data suggested that different starch sources affected (p < 0.05) the metabolic patterns of liver. Compared with the TS diet, the PS diet increased (p < 0.05) some unsaturated fatty acids and several amino acids or peptide levels in the liver of pigs. Moreover, transcriptome data indicated the PS diets elevated (p < 0.05) fatty acid β-oxidation-related gene expression in the liver of pigs, and reduced (p < 0.05) unsaturated fatty acid metabolism-related gene expression. The results of quantitative real-time PCR confirmed that the PS diet upregulated (p < 0.05) the expression of acyl-CoA dehydrogenase very long chain (ACADVL), carnitine palmitoyl transferase (CPT) 1A, and malonyl-CoA decarboxylase (MLYCD), and downregulated (p < 0.05) the expression level of cytochrome P450 2U1 (CYP2U1) and aldehyde dehydrogenase 1B1 (ALDH1B1) in the liver. In addition, the results of a Mantel test indicated the muscle fatty acids were significantly closely correlated (p < 0.05) with liver gene expressions and metabolites. In summary, these findings suggest that diets containing higher amylose starches improved the lipid degradation and the unsaturated fatty acid levels in pig livers, and thus can generate some potential beneficial effects (such as anti-inflammatory and antioxidant) on pig health.},
}
@article {pmid39595229,
year = {2024},
author = {Gao, G and Jiao, Y and Kwok, LY and Zhong, Z},
title = {Gut Microbiome-Host Genetics Co-Evolution Shapes Adiposity by Modulating Energy and Lipid Metabolism in Selectively Bred Broiler Chickens.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/ani14223174},
pmid = {39595229},
issn = {2076-2615},
support = {SPKJ202208//the Science and Technology Programs of College of Food Science and Engineering, Inner Mongolia Agricultural University/ ; 2022110//Research support funds for high-level talents in public institutions at the autonomous region level in Inner Mongolia in 2022/ ; },
abstract = {Optimizing fat deposition is crucial for improving chicken production and meat quality. This study investigated the interactive roles of host genetics and gut microbiome in regulating abdominal fat deposition in selectively bred broiler chicken lines. We compared the gut microbiome composition and host whole-genome profiles between fat-line and lean-line broiler chickens that had been selectively bred for divergent abdominal fat levels over 15 generations. Despite identical dietary and environmental conditions, the two chicken lines exhibited significant differences in their gut microbiota. Lean-line broiler chickens exhibited an increased abundance of intestinal Lactobacillus and a decreased presence of potentially pathogenic species, such as Campylobacter coli, Corynebacterium casei, and Enterococcus faecalis. These microbial alterations were accompanied by shifts in the functional metagenome, with enrichment in pathways involved in energy metabolism and nutrient utilization in the lean-line chickens. Notably, the selective breeding process also led to genomic variations in the lean broilers, with single nucleotide polymorphisms predominantly observed in genes related to energy and lipid metabolism. Our findings suggest that the host-microbiome interactions play a key role in the divergent abdominal fat deposition phenotypes observed in these selectively bred chicken lines. The co-evolution of the gut microbiome and host genetics highlights the importance of considering both factors to optimize poultry production efficiency and meat quality. This study offers new insights into the intricate gut-genome interactions in chicken fat metabolism, paving the way for more effective breeding and microbiome-based strategies to manage adiposity in poultry.},
}
@article {pmid39593380,
year = {2024},
author = {Cardinali, F and Rampanti, G and Paderni, G and Milanović, V and Ferrocino, I and Reale, A and Boscaino, F and Raicevic, N and Ilincic, M and Osimani, A and Aquilanti, L and Martinovic, A and Garofalo, C},
title = {A comprehensive study on the autochthonous microbiota, volatilome, physico-chemical, and morpho-textural features of Montenegrin Njeguški cheese.},
journal = {Food research international (Ottawa, Ont.)},
volume = {197},
number = {Pt 1},
pages = {115169},
doi = {10.1016/j.foodres.2024.115169},
pmid = {39593380},
issn = {1873-7145},
mesh = {*Cheese/microbiology/analysis ; *Food Microbiology ; *Microbiota ; *Volatile Organic Compounds/analysis ; *Biogenic Amines/analysis ; Montenegro ; Bacteria/classification ; Odorants/analysis ; },
abstract = {The present study aims to deepen the knowledge of the microbiota, gross composition, physico-chemical and morpho-textural features, biogenic amines content and volatilome of Njeguški cheese, one of the most popular indigenous cheeses produced in Montenegro. Cheese samples were collected in duplicate from three different batches produced by three Montenegrin artisan producers. For the first time, the microbiota of Njeguški cheese was investigated using both culture-dependent techniques and metagenomic analysis. Coagulase positive staphylococci viable counts were below the detection limit of the analysis (<1 log cfu g[-1]). Salmonella spp., Listeria monocytogenes and staphylococcal enterotoxins were absent. However, relatively high viable counts of Enterobacteriaceae, Escherichia coli, Pseudomonadaceae and eumycetes were detected. Metataxonomic analysis revealed a core microbiome composed of Lactococcus lactis, Streptococcus thermophilus, Debaryomyces hansenii, and Kluyveromyces marxianus. Furthermore, the detection of opportunistic pathogenic yeasts such as Magnusiomyces capitatus and Wickerhamiella pararugosa, along with the variable content of biogenic amines, suggests the need for increased attention to hygienic conditions during Njeguški cheese production. Significant variability was observed in humidity (ranging from 38.37 to 45.58 %), salt content (ranging from 0.70 to 1.78 %), proteins content (ranging from 21.42 to 25.08 %), ash content (ranging from 2.97 to 4.05 %), hardness, springiness, and color among samples from different producers. Gas chromatography-mass spectrometry analysis showed a well-defined and complex volatilome profile of the Njeguški cheese, with alcohols (ethanol, isoamyl alcohol, phenetyl alcol), esters and acetates (ethyl acetate, ethyl butanoate, isoamyl acetate), ketones (acetoin, 2-butanone), and acids (acetic, butanoic, hexanoic acids) being the main chemical groups involved in aroma formation. This research will provide new insights into the still poorly explored identity of Njeguški cheese, thus serving as a first baseline for future studies aimed at protecting its tradition.},
}
@article {pmid39593354,
year = {2024},
author = {Peng, Q and Zheng, H and Zhou, H and Chen, J and Xu, Y and Wang, Z and Xie, G},
title = {Elucidating core microbiota in yellow wine (Huangjiu) through flavor-oriented synthesis and construction of microbial communities.},
journal = {Food research international (Ottawa, Ont.)},
volume = {197},
number = {Pt 1},
pages = {115139},
doi = {10.1016/j.foodres.2024.115139},
pmid = {39593354},
issn = {1873-7145},
mesh = {*Volatile Organic Compounds/analysis ; *Fermentation ; *Microbiota ; *Wine/analysis/microbiology ; *Taste ; Humans ; Gas Chromatography-Mass Spectrometry ; Solid Phase Microextraction ; Pentanols/metabolism/analysis ; Odorants/analysis ; Flavoring Agents/analysis ; China ; Male ; Saccharomyces cerevisiae/metabolism ; Food Microbiology ; Female ; Phenylethyl Alcohol/metabolism/analysis ; Adult ; Butanols ; },
abstract = {Huangjiu, a traditional Chinese alcoholic beverage with a history spanning thousands of years, holds significant cultural and economic value in China. Despite its importance, the complexity of Huangjiu fermentation and the intricate interactions within its microbial community remain underexplored. This study addresses this gap by identifying the core volatile organic compounds (VOCs) and key microorganisms that define the flavor profile of Huangjiu. We employed HS-SPME-GC-MS along with aroma reconstitution and omission experiments to identify core VOCs, including Isobutanol, Isoamyl alcohol, β-Phenylethanol, and others. Metagenomic sequencing combined with QPCR was used to analyze microbial communities, revealing the temporal and spatial dynamics during fermentation. A synthetic microbial community model was constructed using the core microbes identified: Saccharomyces cerevisiae, Lactobacillus brevis, Saccharopolyspora rectivirgula, Bacillus subtilis, Leuconostoc citreum, Lactobacillus plantarum, Lactobacillus curvatus, Lactobacillus casei, and Aspergillus oryzae. This model successfully replicated Huangjiu's core VOCs and sensory characteristics, increased alcohol content, and reduced acidity. Our study contributes valuable insights into the microbial influences on Huangjiu quality, paving the way for its enhanced production and providing a foundation for future research in fermented beverages.},
}
@article {pmid39593339,
year = {2024},
author = {Scarano, L and Peruzy, MF and Fallico, V and Blaiotta, G and Aponte, M and Anastasio, A and Murru, N},
title = {Provolone del Monaco PDO cheese: Lactic microflora, biogenic amines and volatilome characterization.},
journal = {Food research international (Ottawa, Ont.)},
volume = {197},
number = {Pt 1},
pages = {115257},
doi = {10.1016/j.foodres.2024.115257},
pmid = {39593339},
issn = {1873-7145},
mesh = {*Cheese/microbiology/analysis ; *Biogenic Amines/analysis/metabolism ; *Volatile Organic Compounds/analysis/metabolism ; *Food Microbiology ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Bacteriocins ; Tyramine/analysis/metabolism ; Lactobacillales/metabolism/genetics/isolation &amp; purification ; },
abstract = {One commercial production run of Provolone del Monaco - a long-ripened pasta filata cheese - was followed up to the end of ripening for a total of 20 samples. 371 LAB isolates were subject to genetic characterization followed by 16S rRNA gene sequencing. The dominant species were Lacticaseibacillus casei/paracasei (19.4 %), Streptococcus macedonicus (19.1 %) and Enterococcus faecalis (13.2 %). Strains were screened for features of technological interest or safety relevance. Tyramine-producing cultures were quite common, above all within enterococci. By MALDI TOF Mass Spectrometry, one Lactococcus lactis and one Enterococcus faecium strain proved to be bacteriocin producers. Four further cheese wheels from the same production run at 623 days of ripening were evaluated for volatile organic compounds, biogenic amines, and bacterial community by metagenomic sequencing. Three individual wheel samples shared a rather similar microbiome with Lactobacillus delbrueckii and Streptococcus thermophilus as the most represented species, while the fourth wheel appeared wholly different being dominated by Lentilactobacillus buchneri and St. infantarius. Additionally, this sample had the greatest content of biogenic amines and a different VOCs composition. Given the variance seen among cheese wheels processed and ripened under the same conditions, the search for adjunct cultures in the production of this cheese seems to be of utmost importance.},
}
@article {pmid39593310,
year = {2024},
author = {Li, X and Du, C and Zhao, Y and Li, J and Hu, Y and Dong, W and Peng, N and Zhao, S},
title = {Differences in microbial communities among different types of zaopei and their effects on quality and flavor of baijiu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {197},
number = {Pt 1},
pages = {115224},
doi = {10.1016/j.foodres.2024.115224},
pmid = {39593310},
issn = {1873-7145},
mesh = {*Fermentation ; *Microbiota ; *Food Microbiology ; *Taste ; Ethanol/metabolism ; Fermented Foods/microbiology ; Lactobacillales/genetics/metabolism/classification ; Lactic Acid/metabolism/analysis ; Fungi/classification/genetics ; Acetic Acid/metabolism/analysis ; Oryza/microbiology ; Bacteria/classification/genetics/metabolism ; Flavoring Agents/analysis ; },
abstract = {Three types of zaopei (fermented grain) of xiaoqu light-flavor baijiu (XQZP), daqu light-flavor baijiu (DQZP), and strong-flavor baijiu (SFZP) at the end of fermentation and their dominant lactic acid bacteria were systematically compared and analyzed in this study. The results showed that these three types of zaopei differed significantly in acidity, reducing sugar content, and ethanol content, and that the main factors influencing their microbial community were acidity and lactic acid. The diversity and contents of flavor substances were significantly higher in SFZP than in DQZP and XQZP. Additionally, there was a strong correlation between dominant lactic acid bacteria and flavor substances in all three zaopei, but the correlation between fungi and flavor substances was higher than that between bacteria and flavor substances. Differential gene analysis revealed that the microbial activities followed the order of SFZP > DQZP > XQZP. The KEGG enrichment analysis indicated that the differential genes from different zaopei were enriched in different metabolic pathways. Furthermore, various microorganisms in 3 types of zaopei contained different functional genes, of which fungi mainly contained genes responsible for the synthesis of ethanol and acetic acid, while lactic acid bacteria mainly contained genes responsible for the synthesis of lactic acid. In XQZP, L. helveticus was dominant lactic acid bacteria prominent in acetic acid tolerance and lactic acid production; in DQZP, L. acetotolerans was remarkable in its tolerance to lactic acid, acetic acid, ethanol and lactic acid production; and in SFZP, A. jinshanensis was superior in acetic acid tolerance and production. Taken together, this study reveals the mechanism underlying flavor differences among three types of baijiu and provides valuable references for the development and utilization of baijiu microbial resources.},
}
@article {pmid39592704,
year = {2024},
author = {Hai, C and Hao, Z and Bu, L and Lei, J and Liu, X and Zhao, Y and Bai, C and Su, G and Yang, L and Li, G},
title = {Increased rumen Prevotella enhances BCAA synthesis, leading to synergistically increased skeletal muscle in myostatin-knockout cattle.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1575},
pmid = {39592704},
issn = {2399-3642},
support = {32360837, 32341052//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; Cattle ; *Myostatin/genetics/metabolism ; *Amino Acids, Branched-Chain/metabolism/biosynthesis ; *Prevotella/genetics/metabolism ; *Muscle, Skeletal/metabolism ; *Rumen/microbiology/metabolism ; Gene Knockout Techniques ; Gastrointestinal Microbiome/genetics ; },
abstract = {Myostatin (MSTN) is a negative regulator of muscle growth, and its relationship with the gut microbiota is not well understood. In this study, we observed increase muscle area and branched-chain amino acids (BCAAs), an energy source of muscle, in myostatin knockout (MSTN-KO) cattle. To explore the link between increased BCAAs and rumen microbiota, we performed metagenomic sequencing, metabolome analysis of rumen fluid, and muscle transcriptomics. MSTN-KO cattle showed a significant increase in the phylum Bacteroidota (formerly Bacteroidetes), particularly the genus Prevotella (P = 3.12e-04). Within this genus, Prevotella_sp._CAG:732, Prevotella_sp._MSX73, and Prevotella_sp._MA2016 showed significant upregulation of genes related to BCAA synthesis. Functional enrichment analysis indicated enrichment of BCAA synthesis-related pathways in both rumen metagenomes and metabolomes. Additionally, muscle transcriptomics indicated enrichment in muscle fiber and amino acid metabolism, with upregulation of solute carrier family genes, enhancing BCAA transport. These findings suggest that elevated rumen Prevotella in MSTN-KO cattle, combined with MSTN deletion, synergistically improves muscle growth through enhanced BCAA synthesis and transport.},
}
@article {pmid39592438,
year = {2024},
author = {Zhang, S and Wen, H and Chen, Y and Ning, J and Hu, D and Dong, Y and Yao, C and Yuan, B and Yang, S},
title = {Crosstalk between gut microbiota and tumor: tumors could cause gut dysbiosis and metabolic imbalance.},
journal = {Molecular oncology},
volume = {},
number = {},
pages = {},
doi = {10.1002/1878-0261.13763},
pmid = {39592438},
issn = {1878-0261},
support = {82303747//National Natural Science Foundation of China/ ; 2020GXLH-Y-010//Key Research and Development Projects of Shaanxi Province/ ; 2022JM-509//Natural Science Basic Research Program of Shaanxi Province/ ; },
abstract = {Gut microbiota has a proven link with the development and treatment of cancer. However, the causality between gut microbiota and cancer development is still unknown and deserves exploration. In this study, we aimed to explore the alterations in gut microbiota in murine tumor models and the crosstalk between the tumor and the gut microbiota. The subcutaneous and intravenous murine tumor models using both the colorectal cancer cell line MC38 and lung cancer cell line LLC were constructed. Then fecal samples before and after tumor inoculation were collected for whole metagenomics sequencing. Both subcutaneous and metastatic tumors markedly elevated the α-diversity of the gut microbiota. Relative abundance of Ligilactobacillus and Lactobacillus was reduced after subcutaneously inoculating tumor cells, whereas Bacteroides and Duncaniella were reduced in metastatic tumors, regardless of tumor type. At the species level, Lachnospiraceae bacterium was enriched after both subcutaneous and intravenous tumors inoculation, whereas levels of Muribaculaceae bacterium Isolate-110 (HZI), Ligilactobacillus murinus and Bacteroides acidifaciens reduced. Metabolic function analysis showed that the reductive pentose phosphate cycle, urea cycle, ketone body biosynthesis, ectoine biosynthesis, C4-dicarboxylic acid cycle, isoleucine biosynthesis, inosine 5'-monophosphate (IMP), and uridine 5'-monophosphate (UMP) biosynthesis were elevated after tumor inoculation, whereas the cofactor and vitamin biosynthesis were deficient. Principal coordinates analysis (PCoA) showed that subcutaneous and metastatic tumors partially shared the same effect patterns on gut microbiota. Furthermore, fecal microbiota transplantation revealed that this altered microbiota could influence tumor growth. Taken together, this study demonstrated that both colorectal cancer (MC38) and non-colorectal cancer (LLC) can cause gut dysbiosis and metabolic imbalance, regardless of tumor type and process of tumor inoculation, and this dysbiosis influenced the tumor growth. This research gives novel insights into the crosstalk between tumors and the gut microbiota.},
}
@article {pmid39591974,
year = {2024},
author = {Peng, Y and Zhu, J and Wang, S and Liu, Y and Liu, X and DeLeon, O and Zhu, W and Xu, Z and Zhang, X and Zhao, S and Liang, S and Li, H and Ho, B and Ching, JY and Cheung, CP and Leung, TF and Tam, WH and Leung, TY and Chang, EB and Chan, FKL and Zhang, L and Ng, SC and Tun, HM},
title = {A metagenome-assembled genome inventory for children reveals early-life gut bacteriome and virome dynamics.},
journal = {Cell host &amp; microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2024.10.017},
pmid = {39591974},
issn = {1934-6069},
abstract = {Existing microbiota databases are biased toward adult samples, hampering accurate profiling of the infant gut microbiome. Here, we generated a metagenome-assembled genome inventory for children (MAGIC) from a large collection of bulk and viral-like particle-enriched metagenomes from 0 to 7 years of age, encompassing 3,299 prokaryotic and 139,624 viral species-level genomes, 8.5% and 63.9% of which are unique to MAGIC. MAGIC improves early-life microbiome profiling, with the greatest improvement in read mapping observed in Africans. We then identified 54 candidate keystone species, including several Bifidobacterium spp. and four phages, forming guilds that fluctuated in abundance with time. Their abundances were reduced in preterm infants and were associated with childhood allergies. By analyzing the B. longum pangenome, we found evidence of phage-mediated evolution and quorum sensing-related ecological adaptation. Together, the MAGIC database recovers genomes that enable characterization of the dynamics of early-life microbiomes, identification of candidate keystone species, and strain-level study of target species.},
}
@article {pmid39591767,
year = {2024},
author = {Geng, Q and Wang, Z and Shi, T and Wen, C and Xu, J and Jiao, Y and Diao, W and Gu, J and Wang, Z and Zhao, L and Deng, T and Xiao, C},
title = {Cannabidiol regulates L-carnitine and butyric acid metabolism by modulating the gut microbiota to ameliorate collagen-induced arthritis.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {136},
number = {},
pages = {156270},
doi = {10.1016/j.phymed.2024.156270},
pmid = {39591767},
issn = {1618-095X},
abstract = {BACKGROUND: Rheumatoid arthritis (RA) is one of the most common autoimmune diseases, affecting multiple systems in the body. Cannabidiol (CBD) is one of the most medically valuable active ingredients in cannabis. At present, CBD has been shown to alleviate the progression of RA; however, owing to its multiple targets, the mechanism of CBD is not clear.<br><br>METHODS: On the basis of the gut microbiota, we explored the mechanism by which CBD inhibits RA progression. Metagenomic and nontargeted metabolomic analyses were used to determine the changes in the intestinal ecology and plasma metabolites of collagen-induced arthritis (CIA) rats after CBD treatment.<br><br>RESULTS: CBD reversed gut dysbiosis in CIA rats, notably altering the abundances of Allobaculum_unclassified, Allobaculum_fili, and Prevotella_unclassified. In addition, metabolomic analysis confirmed that CBD increased the contents of butyric acid and L-carnitine. Allobaculum could produce butyric acid and Prevotella could accelerate the metabolism of L-carnitine. In addition, in vitro experiments demonstrated that L-carnitine participated in the regulation of neutrophils, macrophages and RA-fibroblast-like synoviocytes (RA-FLSs), which was consistent with the synovial changes in CIA rats caused by CBD.<br><br>CONCLUSION: In summary, CBD increased the plasma contents of butyric acid and L-carnitine by altering the abundances of gut microbiota, thereby inhibiting inflammation in neutrophils, macrophages and RA-FLSs. Our study is the first to explain the mechanism by which CBD alleviates progression in CIA rats from the perspective of gut microbes and metabolites, providing new views into CBD mechanisms, which warrants clinical attention.},
}
@article {pmid39591453,
year = {2024},
author = {Wang, L and Liu, Y and Ni, H and Zuo, W and Shi, H and Liao, W and Liu, H and Chen, J and Bai, Y and Yue, H and Huang, A and Friedman, J and Si, T and Liu, Y and Chen, M and Dai, L},
title = {Systematic characterization of plant-associated bacteria that can degrade indole-3-acetic acid.},
journal = {PLoS biology},
volume = {22},
number = {11},
pages = {e3002921},
doi = {10.1371/journal.pbio.3002921},
pmid = {39591453},
issn = {1545-7885},
abstract = {Plant-associated microbiota affect pant growth and development by regulating plant hormones homeostasis. Indole-3-acetic acid (IAA), a well-known plant hormone, can be produced by various plant-associated bacteria. However, the prevalence of bacteria with the capacity to degrade IAA in the rhizosphere has not been systematically studied. In this study, we analyzed the IAA degradation capabilities of bacterial isolates from the roots of Arabidopsis and rice. Using genomics analysis and in vitro assays, we found that 21 out of 183 taxonomically diverse bacterial isolates possess the ability to degrade IAA. Through comparative genomics and transcriptomic assays, we identified iac-like or iad-like operon in the genomes of these IAA degraders. Additionally, the putative regulator of the operon was found to be highly conserved among these strains through protein structure similarity analysis. Some of the IAA degraders could utilize IAA as their carbon and energy source. In planta, most of the IAA degrading strains mitigated Arabidopsis and rice seedling root growth inhibition (RGI) triggered by exogenous IAA. Moreover, RGI caused by complex synthetic bacterial community can be alleviated by introducing IAA degraders. Importantly, we observed increased colonization preference of IAA degraders from soil to root according to the frequency of the biomarker genes in metagenome-assembled genomes (MAGs) collected from different habitats, suggesting that there is a close association between IAA degraders and IAA producers. In summary, our findings further the understanding of the functional diversity and potential biological roles of plant-associated bacteria in host plant root morphogenesis.},
}
@article {pmid39590379,
year = {2024},
author = {Fernández, M and Barahona, S and Gutierrez, F and Alcaíno, J and Cifuentes, V and Baeza, M},
title = {Bacterial Diversity, Metabolic Profiling, and Application Potential of Antarctic Soil Metagenomes.},
journal = {Current issues in molecular biology},
volume = {46},
number = {11},
pages = {13165-13178},
doi = {10.3390/cimb46110785},
pmid = {39590379},
issn = {1467-3045},
support = {RG_02-18//Instituto Antartico Chileno/ ; ENL03/22//Vicerrectoria de Investigacion y Desarrollo, Universidad de Chile./ ; },
abstract = {Antarctica has attracted increasing interest in understanding its microbial communities, metabolic potential, and as a source of microbial hydrolytic enzymes with industrial applications, for which advances in next-generation sequencing technologies have greatly facilitated the study of unculturable microorganisms. In this work, soils from seven sub-Antarctic islands and Union Glacier were studied using a whole-genome shotgun metagenomic approach. The main findings were that the microbial community at all sites was predominantly composed of the bacterial phyla Actinobacteria and Cyanobacteria, and the families Streptomycetaceae and Pseudonocardiaceae. Regarding the xenobiotic biodegradation and metabolism pathway, genes associated with benzoate, chloroalkane, chloroalkene, and styrene degradation were predominant. In addition, putative genes encoding industrial enzymes with predicted structural properties associated with improved activity at low temperatures were found, with catalases and malto-oligosyltrehalose trehalohydrolase being the most abundant. Overall, our results show similarities between soils from different Antarctic sites with respect to more abundant bacteria and metabolic pathways, especially at higher classification levels, regardless of their geographic location. Furthermore, our results strengthen the potential of Antarctic soils as a source of industrially relevant enzymes.},
}
@article {pmid39589660,
year = {2024},
author = {Xue, X and Zhao, Z and Zhao, LB and Gao, YH and Xu, WH and Cai, WM and Chen, SH and Li, TJ and Nie, TY and Rui, D and Ma, Y and Qian, XS and Lin, JL and Liu, L},
title = {Gut microbiota changes in healthy individuals, obstructive sleep apnea patients, and patients treated using continuous positive airway pressure: a whole-genome metagenomic analysis.},
journal = {Sleep &amp; breathing = Schlaf &amp; Atmung},
volume = {29},
number = {1},
pages = {11},
pmid = {39589660},
issn = {1522-1709},
support = {22BJZ52//Military Health Care Project/ ; 23BJZ27//Military Health Care Project/ ; SYDW_KY[2021]04//Military experimental animal special research project/ ; },
mesh = {Humans ; *Continuous Positive Airway Pressure ; *Sleep Apnea, Obstructive/therapy/microbiology ; *Gastrointestinal Microbiome/physiology/genetics ; Male ; Middle Aged ; Female ; Adult ; *Metagenomics ; Polysomnography ; },
abstract = {PURPOSE: This study investigated variations in gut microbiota among severe obstructive sleep apnea (OSA) patients and changes in gut microbiota after continuous positive airway pressure (CPAP) treatment.<br><br>METHOD: From November 2020 to August 2021, laboratory-based polysomnography (PSG) was used to measure sleep parameters in healthy controls, severe OSA patients, and severe OSA patients treated with CPAP for three months. A fully automated biochemical analyzer was used to evaluate routine blood tests and biochemical indicators. Whole-genome metagenomic analysis was used to determine the microbial composition of gut samples from all participants. The relationships between gut microbiota and hypertension were examined using correlation analysis.<br><br>RESULT: The relative abundances of Bacteroides, Firmicutes, and Parabacteroides were significantly lower at the species level. Enterobacterales and Turicibacter were significantly higher in participants with severe OSA than healthy controls. Negative correlations were identified between Bacteroides coprocola and systolic blood pressure (SBP) (r&#x2009;=&#x2009;&#x2009;-&#x2009;0.710, P&#x2009;=&#x2009;0.003) and diastolic blood pressure (DBP) (r&#x2009;=&#x2009;&#x2009;-&#x2009;0.615, P&#x2009;=&#x2009;0.015). Conversely, a positive correlation was found between Escherichia coli and SBP (r&#x2009;=&#x2009;0.568, P&#x2009;=&#x2009;0.027).<br><br>CONCLUSION: The metabolic pathways and gut microbiota differed significantly between the control group and individuals with severe OSA. Additionally, CPAP therapy substantially changed the metabolic pathways and gut microbial composition among patients diagnosed with severe OSA. Correlation analysis further revealed a strong association between Escherichia coli, Bacteroides coprocola, and blood pressure levels.},
}
@article {pmid39589588,
year = {2024},
author = {Wanna, W and Aucharean, C and Jaeram, N},
title = {Analysis of Gut Microbiota Associated with WSSV Resistance in Litopenaeus vannamei.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {27},
number = {1},
pages = {10},
pmid = {39589588},
issn = {1436-2236},
support = {SCI6601054S//The National Science, Research and Innovation Fund (NSRF) and Prince of Songkla University/ ; SCI6601054S//The National Science, Research and Innovation Fund (NSRF) and Prince of Songkla University/ ; PSU_PHD2565-004//The Graduate School, Prince of Songkla University/ ; },
mesh = {Animals ; *Penaeidae/microbiology/virology ; *White spot syndrome virus 1/genetics ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; Disease Resistance/genetics ; Metagenome ; },
abstract = {Microorganisms in the digestive tract regulate the metabolism of host cells as well as stimulate the immune system of the host. If the microbiota is in good balance, it will promote the good health of the host. In this study, using 16S rRNA sequencing, we analyzed the microbiota of three groups of shrimp: a group of normal shrimp (control group), shrimp that were killed by infection with the white spot syndrome virus (WSSV) (susceptible group), and shrimp that survived WSSV infection (resistant group). The results showed that although the alpha diversity of the microbiota was barely affected by the WSSV, the bacterial communities in the three groups had different prevalences. The resistant group harbored significantly more bacteria than both the other groups. Remarkably, the resistant group had the greatest prevalence of the phylum Bacterioidetes, the families Rhodobacteraceae and Flavobacteriaceae, and the genus Nautella, suggesting their potential as biomarkers for shrimp resistance to WSSV infection. In addition, analysis of functional diversity in bacterial communities showed that the abundance of bacterial metagenomes in two groups infected with WSSV was mostly linked to metabolism and cellular processes. The susceptible WSSV group exhibited a significant reduction in amino acid metabolism. This result suggested that metabolism was the principal factor affecting the alteration in the microbiota after WSSV infection. This overview of the gut microbiota of shrimp infected with the WSSV offers crucial insights for aquaculture management and simplifies the use of control strategies in the future.},
}
@article {pmid39589125,
year = {2024},
author = {Zhang, Z and Tong, M and Ding, W and Liu, S and Jong, M-C and Radwan, AA and Cai, Z and Zhou, J},
title = {Changes in the diversity and functionality of viruses that can bleach healthy coral.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0081624},
doi = {10.1128/msphere.00816-24},
pmid = {39589125},
issn = {2379-5042},
abstract = {UNLABELLED: Coral microbiomes play a crucial role in maintaining the health and functionality of holobionts. Disruption in the equilibrium of holobionts, including bacteria, fungi, and archaea, can result in the bleaching of coral. However, little is known about the viruses that can infect holobionts in coral, especially bacteriophages. Here, we employed a combination of amplicon and metagenomic analyses on Acropora muricata and Galaxea astreata to investigate the diversity and functionality of viruses in healthy and bleached corals. Analysis showed that the alpha diversity of holobionts (bacteria, eukaryotes, zooxanthellae, and lysogenic and lytic viruses) was higher in bleached corals than that in healthy corals. Meanwhile, bleached corals exhibited a relatively higher abundance of specific viral classes, including Revtraviricetes, Arfiviricetes, Faserviricetes, Caudoviricetes, Herviviricetes, and Tectiliviricetes; moreover, we found that the expression levels of functional genes involved in carbon and sulfur metabolism were enriched. An increase in Vibrio abundance has been reported as a notable factor in coral bleaching; our analysis also revealed an increased abundance of Vibrio in bleached coral. Finally, bleached corals contained a higher abundance of Vibrio phages and encoded more virulence factor genes to increase the competitiveness of Vibrio after coral bleaching. In conclusion, we attempted to understand the causes of coral bleaching from the perspective of phage-bacteria-coral tripartite interaction.<br><br>IMPORTANCE: Viruses, especially bacteriophages, outnumber other microorganisms by approximately 10-fold and represent the most abundant members of coral holobionts. Corals represent a model system for the study of symbiosis, the influence of viruses on organisms inhabiting healthy coral reef, the role of rapid horizontal gene transfer, and the expression of auxiliary metabolic genes. However, the least studied component of coral holobiont are viruses. Therefore, there is a critical need to investigate the viral community of viruses, and their functionality, in healthy and bleached coral. Here, we compared the composition and functionality of viruses in healthy and bleached corals and found that viruses may participate in the induction of coral bleaching by enhancing the expression of virulence genes and other auxiliary metabolic functions.},
}
@article {pmid39588334,
year = {2024},
author = {Zhang, J and Wu, L and Zhang, Z and Li, D and Han, R and Ye, L and Zhang, Y and Hong, J and Gu, W},
title = {Gut microbiota and metabolic profiles in adults with unclassified diabetes: a cross-sectional study.},
journal = {Frontiers in endocrinology},
volume = {15},
number = {},
pages = {1440984},
pmid = {39588334},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Adult ; Case-Control Studies ; Cross-Sectional Studies ; *Diabetes Mellitus, Type 2/microbiology/metabolism/blood ; *Metabolome ; Diabetes Mellitus, Type 1/microbiology/metabolism/blood ; Biomarkers/blood ; Young Adult ; },
abstract = {AIMS: Our study, employing a multi-omics approach, aimed to delineate the distinct gut microbiota and metabolic characteristics in individuals under 30 with unclassified diabetes, thus shedding light on the underlying pathophysiological mechanisms.<br><br>METHODS: This age- and sex-matched case-control study involved 18 patients with unclassified diabetes, 18 patients with classic type 1 diabetes, 13 patients with type 2 diabetes, and 18 healthy individuals. Metagenomics facilitated the profiling of the gut microbiota, while untargeted liquid chromatography-mass spectrometry was used to quantify the serum lipids and metabolites.<br><br>RESULTS: Our findings revealed a unique gut microbiota composition in unclassified diabetes patients, marked by a depletion of Butyrivibrio proteoclasticus and Clostridium and an increase in Ruminococcus torques and Lachnospiraceae bacterium 8_1_57FAA. Comparative analysis identified the combined marker panel of five bacterial species, seven serum biomarkers, and three clinical parameters could differentiate patients with UDM from HCs with an AUC of 0.94 (95% CI 0.85-1). Notably, the gut microbiota structure of patients with unclassified diabetes resembled that of type 2 diabetes patients, especially regarding disrupted lipid and branched-chain amino acid metabolism.<br><br>CONCLUSIONS: Despite sharing certain metabolic features with type 2 diabetes, unclassified diabetes presents unique features. The distinct microbiota and metabolites in unclassified diabetes patients suggest a significant role in modulating glucose, lipid, and amino acid metabolism, potentially influencing disease progression. Further longitudinal studies are essential to explore therapeutic strategies targeting the gut microbiota and metabolites to modify the disease trajectory.},
}
@article {pmid39588199,
year = {2024},
author = {Cabrita, ARJ and Barroso, C and Fontes-Sousa, AP and Correia, A and Teixeira, L and Maia, MRG and Vilanova, M and Yergaliyev, T and Camarinha-Silva, A and Fonseca, AJM},
title = {Assessing functional properties of diet protein hydrolysate and oil from fish waste on canine immune parameters, cardiac biomarkers, and fecal microbiota.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1449141},
pmid = {39588199},
issn = {2297-1769},
abstract = {Locally produced fish hydrolysate and oil from the agrifood sector comprises a sustainable solution both to the problem of fish waste disposal and to the petfood sector with potential benefits for the animal's health. This study evaluated the effects of the dietary replacement of mainly imported shrimp hydrolysate (5%) and salmon oil (3%; control diet) with locally produced fish hydrolysate (5%) and oil (3.2%) obtained from fish waste (experimental diet) on systemic inflammation markers, adipokines levels, cardiac function and fecal microbiota of adult dogs. Samples and measurements were taken from a feeding trial conducted according to a crossover design with two diets (control and experimental diets), six adult Beagle dogs per diet and two periods of 6 weeks each. The experimental diet, with higher docosahexaenoic (DHA) and eicosapentaenoic (EPA) acids contents, decreased plasmatic triglycerides and the activity of angiotensin converting enzyme, also tending to decrease total cholesterol. No effects of diet were observed on serum levels of the pro-inflammatory cytokines interleukin (IL)-1β, IL-8, and IL-12/IL-23 p40, and of the serum levels of the anti-inflammatory adipokine adiponectin. Blood pressure, heart rate and echocardiographic measurements were similar between diets with the only exception of left atrial to aorta diameter ratio that was higher in dogs fed the experimental diet, but without clinical relevance. Diet did not significantly affect fecal immunoglobulin A concentration. Regarding fecal microbiome, Megasphaera was the most abundant genus, followed by Bifidobacterium, Fusobacterium, and Prevotella, being the relative abundances of Fusobacterium and Ileibacterium genera positively affected by the experimental diet. Overall, results from the performed short term trial suggest that shrimp hydrolysate and salmon oil can be replaced by protein hydrolysate and oil from fish by-products without affecting systemic inflammatory markers, cardiac structure and function, but potentially benefiting bacterial genera associated with healthy microbiome. Considering the high DHA and EPA contents and the antioxidant properties of fish oil and hydrolysate, it would be worthwhile in the future to assess their long-term effects on inflammatory markers and their role in spontaneous canine cardiac diseases and to perform metabolomic and metagenomics analysis to elucidate the relevance of microbiota changes in the gut.},
}
@article {pmid39587811,
year = {2024},
author = {Xu, N and Chen, B and Wang, Y and Lei, C and Zhang, Z and Ye, Y and Jin, M and Zhang, Q and Lu, T and Dong, H and Shou, J and Penuelas, J and Zhu, YG and Qian, H},
title = {Integrating Anthropogenic-Pesticide Interactions Into a Soil Health-Microbial Index for Sustainable Agriculture at Global Scale.},
journal = {Global change biology},
volume = {30},
number = {11},
pages = {e17596},
doi = {10.1111/gcb.17596},
pmid = {39587811},
issn = {1365-2486},
support = {22376187//National Natural Science Foundation of China/ ; 21777144//National Natural Science Foundation of China/ ; 21976161//National Natural Science Foundation of China/ ; LZ23B070001//Zhejiang Provincial Natural Science Foundation of China/ ; 2021YFA0909500//National Key Research and Development Program of China/ ; MMLKF23-03//Open Funding Project of the State Key Laboratory of Microbial Metabolism/ ; TED2021-132627 B-I00//MCIN, AEI/10.13039/501100011033 European Union Next Generation EU/PRTR/ ; PID2022-140808NB-I00//Spanish Government grants/ ; },
mesh = {*Soil Microbiology ; *Agriculture/methods ; *Pesticides/analysis ; Microbiota ; Sustainable Development ; Soil/chemistry ; Metagenome ; Soil Pollutants/analysis ; Machine Learning ; },
abstract = {Soil microbiota in intensive agriculture are threatened by pesticides, economic activities, and land-use changes. However, the interactions among these anthropogenic factors remain underexplored. By analyzing 2356 soil metagenomes from around the world, we developed a comprehensive soil health-microbial index that integrates microbial diversity, nutrient cycling potential, metabolic potential, primary productivity, and health risks to assess how the soil microbiota respond to anthropogenic factors. Our results indicated that the health-microbial index was the lowest with severe pesticide contamination. Pesticides, in combination with other anthropogenic and climatic factors, exacerbate the decline in this index. Machine learning predictions suggest that the health-microbial index in approximately 26% of global farmland could decline between 2015 and 2040, even under sustainable development scenarios. Even with strategies to reduce pesticide usage, we cannot completely halt the decline in the health-microbial index. Our findings highlight that sustaining soil microbial health on a global scale requires addressing not only pesticide management but also broader anthropogenic impacts.},
}
@article {pmid39587696,
year = {2024},
author = {Cuevas-Martínez, R and González-Chávez, SA and Bermúdez, M and Salas-Leiva, JS and Vázquez-Olvera, G and Hinojos-Gallardo, LC and Chaparro-Barrera, E and Pacheco-Silva, C and Romero-Sánchez, C and Villegas-Mercado, CE and Pacheco-Tena, C},
title = {Intermittent fasting reduces inflammation and joint damage in a murine model of rheumatoid arthritis: insights from transcriptomic and metagenomic analyses.},
journal = {BMC rheumatology},
volume = {8},
number = {1},
pages = {64},
pmid = {39587696},
issn = {2520-1026},
abstract = {BACKGROUND: Intermittent fasting (IF) has shown benefits in various pathological conditions. Although its anti-inflammatory potential has been recognized, its effects on the mechanism underlying rheumatoid arthritis (RA) remain insufficiently characterized. This study aimed to investigate the effects of IF in a murine model of RA.<br><br>METHODS: Collagen-induced arthritis (CIA) was developed in sixteen male DBA/1 mice, randomly assigned to two groups, with one undergoing IF every other day for four weeks. The effects of IF on joint inflammation and remodeling were evaluated clinically, histologically, and through tomography. Transcriptomic changes were characterized using expression microarrays, validated by RT-qPCR, and confirmed by immunohistochemistry. Additionally, modifications in gut microbiota were assessed through 16&#xa0;S sequencing.<br><br>RESULTS: Mice subjected to IF significantly reduced the incidence and severity of clinical arthritis. Histological and radiographic assessments confirmed a decrease in inflammation and joint damage. Transcriptomic analysis revealed that IF led to the upregulation of 364 genes and the downregulation of 543 genes, with notable reductions in inflammatory signaling pathways associated with RA-related genes, including Cd72, Cd79a, Ifna, Il33, and Bglap 2. Notably, IL33 emerged as a pivotal mediator in the inflammatory processes mitigated by fasting. Key regulators associated with IF effects, such as CEBPA, FOXO1, HIF1A, PPARG, and PPARA, were identified, indicating a complex interplay between metabolic and inflammatory pathways. Furthermore, differential expression of microRNAs and lncRNAs, including miR-15b, miR-103-2, miR-302a, miR-6985, and miR- 5624, was observed. Metagenomic analysis indicated that IF enhanced the abundance and diversity of the gut microbiome, explicitly promoting anti-inflammatory bacterial populations, notably within the genus Ruminococcaceae.<br><br>CONCLUSION: Our findings suggest that IF exerts significant anti-inflammatory and immunoregulatory effects in the context of CIA. Given its non-risky nature, further investigation into the potential benefits of IF in patients with RA is warranted.<br><br>CLINICAL TRIAL NUMBER: Not applicable.},
}
@article {pmid39587555,
year = {2024},
author = {Halford, C and Le Viet, T and Edge, K and Russell, P and Moore, N and Trim, F and Moragues-Solanas, L and Lukaszewski, R and Weller, SA and Gilmour, M},
title = {Development of a clinical metagenomics workflow for the diagnosis of wound infections.},
journal = {BMC medical genomics},
volume = {17},
number = {1},
pages = {276},
pmid = {39587555},
issn = {1755-8794},
support = {BB/CCG1860/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/X011011/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/R015937/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Humans ; *Metagenomics/methods ; *Wound Infection/microbiology/diagnosis ; *Workflow ; Bacteria/genetics/isolation &amp; purification/classification ; },
abstract = {BACKGROUND: Wound infections are a common complication of injuries negatively impacting the patient's recovery, causing tissue damage, delaying wound healing, and possibly leading to the spread of the infection beyond the wound site. The current gold-standard diagnostic methods based on microbiological testing are not optimal for use in austere medical treatment facilities due to the need for large equipment and the turnaround time. Clinical metagenomics (CMg) has the potential to provide an alternative to current diagnostic tests enabling rapid, untargeted identification of the causative pathogen and the provision of additional clinically relevant information using equipment with a reduced logistical and operative burden.<br><br>METHODS: This study presents the development and demonstration of a CMg workflow for wound swab samples. This workflow was applied to samples prospectively collected from patients with a suspected wound infection and the results were compared to routine microbiology and real-time quantitative polymerase chain reaction (qPCR).<br><br>RESULTS: Wound swab samples were prepared for nanopore-based DNA sequencing in approximately 4&#xa0;h and achieved sensitivity and specificity values of 83.82% and 66.64% respectively, when compared to routine microbiology testing and species-specific qPCR. CMg also enabled the provision of additional information including the identification of fungal species, anaerobic bacteria, antimicrobial resistance (AMR) genes and microbial species diversity.<br><br>CONCLUSIONS: This study demonstrates that CMg has the potential to provide an alternative diagnostic method for wound infections suitable for use in austere medical treatment facilities. Future optimisation should focus on increased method automation and an improved understanding of the interpretation of CMg outputs, including robust reporting thresholds to confirm the presence of pathogen species and AMR gene identifications.},
}
@article {pmid39587335,
year = {2024},
author = {Liu, Y and Du, S and Sun, L and Li, Y and Liu, M and Sun, P and Bai, B and Ge, G and Jia, Y and Wang, Z},
title = {Volatile metabolomics and metagenomics reveal the effects of lactic acid bacteria on alfalfa silage quality, microbial communities, and volatile organic compounds.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1565},
pmid = {39587335},
issn = {2399-3642},
mesh = {*Volatile Organic Compounds/metabolism/analysis ; *Silage/microbiology/analysis ; *Metabolomics/methods ; *Microbiota ; *Metagenomics/methods ; *Medicago sativa/microbiology/metabolism ; Lactobacillales/metabolism/genetics ; Lactobacillus plantarum/metabolism/genetics ; },
abstract = {Lactic acid bacteria metabolism affects the composition of volatile organic compounds (VOCs) in alfalfa silage, which results in differences of odor and quality. The aim of this study was to reveal the effects of commercial Lactobacillus plantarum (CL), screened Lactobacillus plantarum (LP), and screened Pediococcus pentosaceus (PP) on quality, microbial community, and VOCs of alfalfa silage based on volatile metabolomics and metagenomics. The results showed that the LP and PP groups had higher sensory and quality grades, and the dominant bacteria were Lactiplantibacillus plantarum and Pediococcus pentosaceus. The main VOCs in alfalfa silage were terpenoids (25.29%), esters (17.08%), and heterocyclic compounds (14.43%), and esters such as methyl benzoate, ethyl benzoate, and ethyl salicylate were significantly increased in the LP and PP groups (P < 0.05). Correlation analysis showed that terpenoids, esters, and alcohols with aromatic odors were positively correlated with Lactiplantibacillus plantarum and Pediococcus pentosaceus. Microbial functions in carbohydrate and amino acid metabolism, biosynthesis of secondary metabolites, and degradation of aromatic compounds were significantly enriched. In conclusion, the addition of lactic acid bacteria can increase the aromatic substances in silage and further improve silage odor and quality.},
}
@article {pmid39587088,
year = {2024},
author = {Honorato, L and Paião, HGO and da Costa, AC and Tozetto-Mendoza, TR and Mendes-Correa, MC and Witkin, SS},
title = {Viruses in the female lower reproductive tract: a systematic descriptive review of metagenomic investigations.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {137},
pmid = {39587088},
issn = {2055-5008},
mesh = {Female ; Humans ; *Metagenomics/methods ; *Viruses/genetics/classification ; *Virome ; Microbiota ; Genitalia, Female/virology/microbiology ; Metagenome ; },
abstract = {The lower female reproductive tract (FRT) hosts a complex microbial environment, including eukaryotic and prokaryotic viruses (the virome), whose roles in health and disease are not fully understood. This review consolidates findings on FRT virome composition, revealing the presence of various viral families and noting significant gaps in knowledge. Understanding interactions between the virome, microbiome, and immune system will provide novel insights for preventing and managing lower genital tract disorders.},
}
@article {pmid39586993,
year = {2024},
author = {Zhao, Y and Bhatnagar, S},
title = {Epigenetic Modulations by Microbiome in Breast Cancer.},
journal = {Advances in experimental medicine and biology},
volume = {1465},
number = {},
pages = {55-69},
doi = {10.1007/978-3-031-66686-5_4},
pmid = {39586993},
issn = {0065-2598},
mesh = {Humans ; *Breast Neoplasms/genetics/microbiology ; *Epigenesis, Genetic ; Female ; *Tumor Microenvironment/genetics ; *Gene Expression Regulation, Neoplastic ; Microbiota/genetics ; Animals ; DNA Methylation ; Gastrointestinal Microbiome/genetics ; },
abstract = {Recent studies have identified a critical role of the diverse and dynamic microbiome in modulating various aspects of host physiology and intrinsic processes. However, the altered microbiome has also become a hallmark of cancer, which could influence the tumor microenvironment. Aberrations in epigenetic regulation of tumor suppressors, apoptotic genes, and oncogenes can accentuate breast cancer onset and progression. Interestingly, recent studies have established that the microbiota modulates the epigenetic mechanisms at global and gene-specific levels. While the mechanistic basis is unclear, the cross-talk between the microbiome and epigenetics influences breast cancer trajectory. Here, we review different epigenetic mechanisms of mammalian gene expression and summarize the host-associated microbiota distributed across the human body and their influence on cancer and other disease-related genes. Understanding this complex relationship between epigenetics and the microbiome holds promise for new insights into effective therapeutic strategies for breast cancer patients.},
}
@article {pmid39498576,
year = {2024},
author = {Meramveliotakis, E and Ortego, J and Anastasiou, I and Vogler, AP and Papadopoulou, A},
title = {Habitat Association Predicts Population Connectivity and Persistence in Flightless Beetles: A Population Genomics Approach Within a Dynamic Archipelago.},
journal = {Molecular ecology},
volume = {33},
number = {23},
pages = {e17577},
doi = {10.1111/mec.17577},
pmid = {39498576},
issn = {1365-294X},
support = {EXCELLENCE/0421/0419//Research and Innovation Foundation/ ; },
mesh = {Animals ; *Coleoptera/genetics ; *Ecosystem ; *Genetics, Population ; *Gene Flow ; *Polymorphism, Single Nucleotide/genetics ; *Population Dynamics ; Islands ; Metagenomics ; Biological Evolution ; },
abstract = {Habitat association has been proposed to affect evolutionary dynamics through its control on dispersal propensity, which is considered a key trait for lineage survival in habitats of low durational stability. The Habitat Constraint hypothesis predicts different micro- and macroevolutionary patterns for stable versus dynamic habitat specialists, but the empirical evidence remains controversial and in insects mostly derives from winged lineages. We here use genome-wide SNP data to assess the effect of habitat association on the population dynamics of two closely related flightless lineages of the genus Eutagenia (Coleoptera: Tenebrionidae), which are co-distributed across the Cyclades islands in the Eastern Mediterranean but are associated with habitat types of different presumed stability: the psammophilous lineage is associated with dynamic sandy coastal habitats, while the geophilous lineage is associated with comparatively stable compact soil habitats. Our comparative population genomic and demographic analyses support higher inter-island gene flow in the psammophilous lineage, presumably due to the physical properties of dynamic sand-dune habitats that promote passive dispersal. We also find consistent bottlenecks in the psammophilous demes, suggesting that lineage evolution in the dynamic habitat is punctuated by local extinction and recolonisation events. The inferred demographic processes are surprisingly uniform among psammophilous demes, but vary considerably among geophilous demes depending on historical island connectivity, indicating more stringent constraints on the dynamic habitat lineage. This study extends the Habitat Constraint hypothesis by demonstrating that selection on dispersal traits is not the only mechanism that can drive consistent differences in evolutionary dynamics between stable versus dynamic habitat specialists.},
}
@article {pmid39586148,
year = {2024},
author = {Jiang, X and Guo, H and Sun, J and Guan, Y and Xie, Z},
title = {Diagnostic value of metagenomic next-generation sequencing for bronchoalveolar lavage diagnostics in patients with lower respiratory tract infections.},
journal = {Diagnostic microbiology and infectious disease},
volume = {111},
number = {2},
pages = {116620},
doi = {10.1016/j.diagmicrobio.2024.116620},
pmid = {39586148},
issn = {1879-0070},
abstract = {BACKGROUND: Current diagnostic methods of lower respiratory tract infections (LRTIs) often lack specificity, underscoring the necessity for advanced technologies such as metagenomic next-generation sequencing (mNGS).<br><br>METHODS: This retrospective study compared bronchoalveolar lavage fluid (BALF) analysis using mNGS and conventional microbiological tests (CMT) to evaluate their effectiveness in pathogen identification and alignment with clinical diagnoses.<br><br>RESULTS: In this study involving 369 patients suspected of LTRIs, mNGS identified pathogens in 342 cases (92.7%), showing superior diagnostic performance compared to CMT (58.8%). The positive agreement and negative agreement rates of mNGS were 92.7% and 96.3%, respectively, both significantly higher than those of CMT (both p<0.001). The sensitivity, specificity, positive predictive value, and negative predictive value of mNGS were significantly higher than those of CMT, with values of 99.7% vs. 57.1%, 68.4% vs. 26.3%, 96.5% vs. 87.1%, and 96.3% vs. 6.3%, respectively (all p<0.001). Pathogen detection rates among the patients showed that 89.7% had evidence of LRTIs, with bacterial infections (20.1%), mycoplasma (13.6%), mycobacterium (4.3%), fungal (4.1%), viral (3.3%), and mixed infections (44.4%) being the most common. Furthermore, the study also differentiated the distribution of pathogens between adults and pediatric patients, and assessed the impact of pathogen types on severe outcomes using multivariate logistic regression, revealing that viral and fungal infections were more likely associated with severe symptoms, whereas mycoplasma infections typically presented with milder symptoms.<br><br>CONCLUSIONS: BALF mNGS proves effective for rapid, comprehensive pathogen detection in LRTIs, warranting its early use for enhanced diagnosis and management, especially across different age groups.},
}
@article {pmid39585984,
year = {2024},
author = {Padhi, C and Field, CM and Forneris, CC and Olszewski, D and Fraley, AE and Sandu, I and Scott, TA and Farnung, J and Ruscheweyh, HJ and Narayan Panda, A and Oxenius, A and Greber, UF and Bode, JW and Sunagawa, S and Raina, V and Suar, M and Piel, J},
title = {Metagenomic study of lake microbial mats reveals protease-inhibiting antiviral peptides from a core microbiome member.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {49},
pages = {e2409026121},
doi = {10.1073/pnas.2409026121},
pmid = {39585984},
issn = {1091-6490},
support = {1-001369-000//Promedica Stiftung/ ; 205320_185077//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; 205320_219638//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; 310030_212802//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; n/a//Peter und Traudl Engelhorn Stiftung (Peter and Traudl Engelhorn Foundation)/ ; 897571//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; },
mesh = {*Lakes/microbiology ; *Antiviral Agents/pharmacology/chemistry ; *Microbiota ; *Metagenomics/methods ; Protease Inhibitors/pharmacology/metabolism ; Peptides/metabolism/chemistry ; Multigene Family ; Metagenome ; India ; Bacteria/drug effects/genetics/metabolism ; },
abstract = {In contrast to the large body of work on bioactive natural products from individually cultivated bacteria, the chemistry of environmental microbial communities remains largely elusive. Here, we present a comprehensive bioinformatic and functional study on a complex and interaction-rich ecosystem, algal-bacterial (microbial) mats of Lake Chilika in India, Asia's largest brackish water body. We report the bacterial compositional dynamics over the mat life cycle, >1,300 reconstructed environmental genomes harboring >2,200 biosynthetic gene clusters (BGCs), the successful cultivation of a widespread core microbiome member belonging to the genus Rheinheimera, heterologous reconstitution of two silent Rheinheimera biosynthetic pathways, and new compounds with potent protease inhibitory and antiviral activities. The identified substances, posttranslationally modified peptides from the graspetide and spliceotide families, were targeted among the large BGC diversity by applying a strategy focusing on recurring multi-BGC loci identified in diverse samples, suggesting their presence in successful colonizers. In addition to providing broad insights into the biosynthetic potential of a poorly studied community from sampling to bioactive substances, the study highlights the potential of ribosomally synthesized and posttranslationally modified peptides as a large, underexplored resource for antiviral drug discovery.},
}
@article {pmid39585972,
year = {2024},
author = {Jaffe, AL and Harrison, K and Wang, RZ and Taylor-Kearney, LJ and Jain, N and Prywes, N and Shih, PM and Young, J and Rocap, G and Dekas, AE},
title = {Cyanobacteria from marine oxygen-deficient zones encode both form I and form II Rubiscos.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {49},
pages = {e2418345121},
doi = {10.1073/pnas.2418345121},
pmid = {39585972},
issn = {1091-6490},
support = {n/a//Stanford Science Fellows/ ; OCE-PRF//NSF (NSF)/ ; OCE-2143035//NSF (NSF)/ ; OCE-2022911//NSF (NSF)/ ; 561645//Simons Foundation (SF)/ ; },
mesh = {*Oxygen/metabolism ; *Ribulose-Bisphosphate Carboxylase/metabolism/genetics ; Seawater/microbiology ; Cyanobacteria/metabolism/genetics ; Carbon Cycle ; Photosynthesis ; Prochlorococcus/metabolism/genetics ; Phylogeny ; Bacterial Proteins/metabolism/genetics ; Carbon Dioxide/metabolism ; Pacific Ocean ; },
abstract = {Cyanobacteria are highly abundant in the marine photic zone and primary drivers of the conversion of inorganic carbon into biomass. To date, all studied cyanobacterial lineages encode carbon fixation machinery relying upon form I Rubiscos within a CO2-concentrating carboxysome. Here, we report that the uncultivated anoxic marine zone (AMZ) IB lineage of Prochlorococcus from pelagic oxygen-deficient zones (ODZs) harbors both form I and form II Rubiscos, the latter of which are typically noncarboxysomal and possess biochemical properties tuned toward low-oxygen environments. We demonstrate that these cyanobacterial form II enzymes are functional in vitro and were likely acquired from proteobacteria. Metagenomic analysis reveals that AMZ IB are essentially restricted to ODZs in the Eastern Pacific, suggesting that form II acquisition may confer an advantage under low-O2 conditions. AMZ IB populations express both forms of Rubisco in situ, with the highest form II expression at depths where oxygen and light are low, possibly as a mechanism to increase the efficiency of photoautotrophy under energy limitation. Our findings expand the diversity of carbon fixation configurations in the microbial world and may have implications for carbon sequestration in natural and engineered systems.},
}
@article {pmid39585730,
year = {2024},
author = {Khleborodova, A and Gamboa-Tuz, SD and Ramos, M and Segata, N and Waldron, L and Oh, S},
title = {Lefser: Implementation of metagenomic biomarker discovery tool, LEfSe, in R.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btae707},
pmid = {39585730},
issn = {1367-4811},
abstract = {SUMMARY: LEfSe is a widely used Python package and Galaxy module for metagenomic biomarker discovery and visualization, utilizing the Kruskal-Wallis test, Wilcoxon Rank-Sum test, and Linear Discriminant Analysis. R/Bioconductor provides a large collection of tools for metagenomic data analysis but has lacked an implementation of this widely-used algorithm, hindering benchmarking against other tools and incorporation into R workflows. We present the lefser package to provide comparable functionality within the R/Bioconductor ecosystem of statistical analysis tools, with improvements to the original algorithm for performance, accuracy, and reproducibility. We benchmark the performance of lefser against the original algorithm using human and mouse metagenomic datasets.<br><br>Our software, lefser, is distributed through the Bioconductor project (https://www.bioconductor.org/packages/release/bioc/html/lefser.html), and all the source code is available in the GitHub repository https://github.com/waldronlab/lefser.<br><br>CONTACT: Institute for Implementation Science in Population Health, Department of Epidemiology and Biostatistics, City University of New York School of Public Health, New York, NY, United States. E-mail: Sehyun.Oh@sph.cuny.edu (S.O.).<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid39584840,
year = {2024},
author = {Bernardin, JR and Young, EB and Gray, SM and Bittleston, LS},
title = {Bacterial community function increases leaf growth in a pitcher plant experimental system.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0129824},
doi = {10.1128/msystems.01298-24},
pmid = {39584840},
issn = {2379-5077},
abstract = {UNLABELLED: Across diverse ecosystems, bacteria and their hosts engage in complex relationships having negative, neutral, or positive interactions. However, the specific effects of leaf-associated bacterial community functions on plant growth are poorly understood. Although microbes can promote plant growth through various biochemical mechanisms, investigating the community's functional contributions to plant growth remains to be explored. To address this gap, we characterized the relationships between bacterial community function and host plant growth in the purple pitcher plant (Sarracenia purpurea). The main aim of our research was to investigate how different bacterial community functions affect the growth and nutrient content in the plant. Previous research has suggested that microbial communities aid in prey decomposition and subsequent nutrient acquisition in carnivorous plants, including S. purpurea. However, the specific functional roles of bacterial communities in plant growth and nutrient uptake are not well known. In this study, sterile, freshly opened pitchers were inoculated with three functionally distinct, pre-assembled bacterial communities. Bacterial community composition and function were measured over 8 weeks using physiological assays, metagenomics, and metatranscriptomics. Distinct community functions affected plant traits; a bacterial community enriched in decomposition was associated with larger leaves with almost double the biomass of control pitchers. Physiological differences in bacterial communities were supported by metatranscriptomics; for example, the bacterial community with the highest chitinase activity had greater expression of transcripts associated with chitinase enzymes. The relationship between bacterial community function and plant growth observed here indicates potential mechanisms, such as chitinase activity, for host-associated bacterial functions to support pitcher plant growth.<br><br>IMPORTANCE: This study addresses a gap in understanding the relationships between bacterial community function and plant growth. We inoculated sterile, freshly opened pitcher plant leaves with three functionally distinct bacterial communities to uncover potential mechanisms through which bacterial functions support plant health and growth. Our findings demonstrate that distinct community functions significantly influence plant traits, with some bacterial communities supporting more plant growth than in control pitchers. These results highlight the ecological roles of microbial communities in plants and thus ecosystems and suggest that nutrient cycling is an important pathway through which microbes support host plant health. This research provides valuable insights into plant-microbe interactions and the effects of diverse microbial community functions.},
}
@article {pmid39584815,
year = {2024},
author = {Holman, DB and Gzyl, KE and Kommadath, A},
title = {Florfenicol administration in piglets co-selects for multiple antimicrobial resistance genes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0125024},
doi = {10.1128/msystems.01250-24},
pmid = {39584815},
issn = {2379-5077},
abstract = {Antimicrobial use in food-producing animals such as pigs is a significant issue due to its association with antimicrobial resistance. Florfenicol is a broad-spectrum phenicol antibiotic used in swine for various indications; however, its effect on the swine microbiome and resistome is largely unknown. This study investigated these effects in piglets treated intramuscularly with florfenicol at 1 and 7 days of age. Fecal samples were collected from treated (n = 30) and untreated (n = 30) pigs at nine different time points up until 140 days of age, and the fecal metagenomes were sequenced. The fecal microbiomes of the two groups of piglets were most dissimilar in the immediate period following florfenicol administration. These differences were driven in part by an increase in the relative abundance of Clostridium scindens, Enterococcus faecalis, and Escherichia spp. in the florfenicol-treated piglets and Fusobacterium spp., Pauljensenia hyovaginalis, and Ruminococcus gnavus in the control piglets. In addition to selecting for florfenicol resistance genes (floR, fexA, and fexB), florfenicol also selected for genes conferring resistance to the aminoglycosides, beta-lactams, or sulfonamides up until weaning at 21 days of age. Florfenicol-resistant Escherichia coli isolated from these piglets were found to carry a plasmid with floR, along with tet(A), aph(6)-Id, aph(3″)-Ib, sul2, and blaTEM-1/blaCMY-2. A plasmid carrying fexB and poxtA (phenicols and oxazolidinones) was identified in florfenicol-resistant Enterococcus avium, Enterococcus faecium, and E. faecalis isolates from the treated piglets. This study highlights the potential for co-selection and perturbation of the fecal microbial community in pre-weaned piglets administered florfenicol.IMPORTANCEAntimicrobial use remains a serious challenge in food-animal production due to its linkage with antimicrobial resistance. Antimicrobial resistance can reduce the efficacy of veterinary treatment and can potentially be transferred to humans through the food chain or direct contact with animals and their environment. In this study, early-life florfenicol treatment in piglets altered the composition of the fecal microbiome and selected for many unrelated antimicrobial resistance genes up until weaning at 21 days of age. Part of this co-selection process appeared to involve an Escherichia coli plasmid carrying a florfenicol resistance gene along with genes conferring resistance to at least four other antimicrobial classes. In addition, florfenicol selected for certain genes that provide resistance to multiple antimicrobial classes, including the oxazolidinones. These results highlight that florfenicol can co-select for multiple antimicrobial resistance genes, and their presence on mobile genetic elements suggests the potential for transfer to other bacteria.},
}
@article {pmid39583548,
year = {2024},
author = {Romero-Yahuitl, V and Zarco-González, KE and Toriz-Nava, AL and Hernández, M and Velázquez-Fernández, JB and Navarro-Noya, YE and Luna-Guido, M and Dendooven, L},
title = {The archaeal and bacterial community structure in composted cow manures is defined by the original populations: a shotgun metagenomic approach.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1425548},
pmid = {39583548},
issn = {1664-302X},
abstract = {INTRODUCTION: Organic wastes are composted to increase their plant nutritional value, but little is known about how this might alter the bacterial and archaeal community structure and their genes.<br><br>METHODS: Cow manure was collected from three local small-scale farmers and composted under controlled conditions, while the bacterial and archaeal communities were determined using shotgun metagenomics at the onset and after 74 days of composting.<br><br>RESULTS: The bacterial, archaeal, methanogen, methanotrophs, methylotroph, and nitrifying community structures and their genes were affected by composting for 74 days, but the original composition of these communities determined the changes. Most of these archaeal and bacterial groups showed considerable variation after composting and between the cow manures. However, the differences in the relative abundance of their genes were much smaller compared to those of the archaeal or bacterial groups.<br><br>DISCUSSION: It was found that composting of different cow manures did not result in similar bacterial or archaeal communities, and the changes that were found after 74 days were defined by the original populations. However, more research is necessary to determine if other composting conditions will give the same results.},
}
@article {pmid39583543,
year = {2024},
author = {Li, Q and Lian, Y and Zhang, K and Chen, J and Chen, L and Wu, J and Zhang, Y and Chen, M and Zhang, W and Lu, M and Ma, J and Bai, A},
title = {Virome of red imported fire ants by metagenomic analysis in Guangdong, southern China.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1479934},
pmid = {39583543},
issn = {1664-302X},
abstract = {The red imported fire ant (RIFA) has made China its habitat for approximately 25 years, but few reports have described the species and amount of virus circulating in it. Researchers are currently exploring viruses associated with RIFAs as potential biological control agents against invasive ants. The present meta-transcriptome analysis revealed the virome of red imported fire ants in Guangdong, southern China, which included 17 viruses, including Solenopsis invicta virus 4-GD (SINV-4) and Guangdong Polycipiviridae ant virus 1 (GPAV1) in the Polycipiviridae family; Solenopsis invicta virus 1-GD (SINV-1), and Guangdong Dicistroviridae ant virus 2-3 (GDAV2-3) in the Dicistroviridae family; Guangdong Iflaviridae ant virus 4-9 (GIAV4-9) in the Iflaviridae family; Guangdong Parvoviridae ant virus 10 (GPAV10) in the Parvoviridae family; and Guangdong ant virus 11-15 (GAV11-15). A total of 15 novel viruses and 2 known viruses were identified in this study. These findings reveal the virome of red imported fire ants in Guangdong Province and present a different result from that of a similar study reported in the United States, providing more choices for potential classical biological control agents against red imported fire ants in China.},
}
@article {pmid39583430,
year = {2024},
author = {Minoretti, P and Fontana, JM and Yilmaz, Y},
title = {Pilots, Astronauts, and the Aerospace Microbiota: A Narrative Review of Occupational Impact.},
journal = {Cureus},
volume = {16},
number = {10},
pages = {e72268},
pmid = {39583430},
issn = {2168-8184},
abstract = {The human microbiota plays a crucial role in maintaining health and preventing disease; however, the effects of occupational exposure on the microbiota of aircrew and astronauts are not fully understood. This narrative review aims to synthesize the current knowledge on microbiota alterations in aerospace medicine, assess the potential of probiotics as a countermeasure, and identify key gaps that warrant further research. The references were identified through searching PubMed for English articles published between 2010 and 2024, using keywords related to microbiota, probiotics, aviation, spaceflight, pilots, and astronauts. Additionally, the bibliographies of relevant papers were reviewed. Studies in aerospace medicine were selected based on their focus on the occupational impact on microbiota and the use of probiotics in this context. For aircrew, initial studies indicate a decrease in beneficial gut bacteria, suggesting that probiotics could enhance gastrointestinal health, immunity, and overall well-being. However, unsupervised use of probiotics carries potential risks. Conversely, spaceflight induces significant changes in the gut, skin, oral, and nasal microbiota of astronauts, characterized by altered diversity and abundance of specific microbial taxa. These changes include a relative decrease in the abundance of beneficial gut bacteria, an increase in opportunistic pathogens, and evidence of microbial transfer between astronauts and spacecraft surfaces. While simulated space studies suggest the potential for probiotics to mitigate dysbiosis, direct testing done during actual spaceflight is lacking. The observed microbiota changes during spaceflight are associated with various health implications, including alterations in metabolic pathways and interactions between the microbial metabolic capabilities and the host's metabolism. In conclusion, this review highlights the profound impact of spaceflight on astronaut microbiota and the promising role of probiotics as an intervention in both space and aviation medicine. However, significant research gaps remain. These include elucidating the functional implications of microbial shifts, developing personalized countermeasures, and validating the efficacy of probiotics during spaceflight. Future studies should leverage advanced tools such as metagenomic analysis and longitudinal tracking of astronaut health to inform targeted interventions that support the well-being of aerospace personnel. Integrating data across different sites of the body and missions, facilitated by resources like the Space Omics and Medical Atlas (SOMA), can help identify consistent microbial changes induced by the unique occupational conditions of spaceflight and aviation. This integrated approach will be crucial for developing effective microbiota-based countermeasures to mitigate the occupational health risks associated with space and aviation.},
}
@article {pmid39583157,
year = {2024},
author = {Guo, RM and Li, XX and Zhou, YH and Liu, YJ and Li, J and Fu, GW and Zhao, H and Zhang, X and Zhao, YC},
title = {Early mNGS testing for diagnose and prognostic prediction of early onset pneumonia among in-hospital cardiac arrest patients undergoing extracorporeal cardiopulmonary resuscitation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1382273},
pmid = {39583157},
issn = {2235-2988},
mesh = {Humans ; Male ; Female ; Middle Aged ; *Extracorporeal Membrane Oxygenation ; Prognosis ; Retrospective Studies ; *Cardiopulmonary Resuscitation ; *Heart Arrest/therapy ; *High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Aged ; Pneumonia/diagnosis ; Bronchoalveolar Lavage Fluid/microbiology ; Adult ; },
abstract = {OBJECTIVES: Metagenomic next-generation sequencing (mNGS) is emerging as a novel diagnostic technology for various infectious diseases; however, limited studies have investigated its application in etiological diagnosis of early onset pneumonia (EOP) among patients undergoing extracorporeal cardiopulmonary resuscitation (ECPR) following in-hospital cardiac arrest (IHCA), The clinical significance of early mNGS in predicting short-term prognosis of IHCA patients after ECPR remains unclear.<br><br>METHODS: This retrospective study included 76 patients with IHCA who underwent ECPR at the First Affiliated Hospital of Zhengzhou University from January 2018 to December 2022. Baseline characteristics and etiological data of all patients during their hospitalization were collected and statistically analyzed. The primary outcome of this study was the diagnosis of EOP, while the secondary outcomes included successful extracorporeal membrane oxygenation (ECMO) weaning and survival at discharge. Additionally, the characteristics of bronchoalveolar lavage fluid (BALF) flora in these patients were compared by analyzing both mNGS results and culture results.<br><br>RESULTS: Multivariate logistic regression were employed to analyze the predictors of ECMO weaning failure, mortality at discharge, and the incidence of EOP. Ultimately, patients with lower SOFA scores on admission [OR (95%CI): 1.447 (1.107-1.890), p=0.007] and those who underwent early mNGS testing within 48 hours after ECPR [OR (95%CI): 0.273 (0.086-0.865), p=0.027] demonstrated a higher probability of successful weaning from ECMO. Patients with higher SOFA scores on admission [OR (95%CI): 2.404 (1.422-4.064), p=0.001], and elevated lactate levels [OR (95%CI): 1.176 (1.017-1.361), p=0.029] exhibited an increased likelihood of mortality at discharge. Furthermore, early mNGS detection [OR (95%CI): 0.186 (0.035-0.979), p=0.047], and lower CRP levels (48h-7d after ECMO) [OR (95%CI):1.011 (1.003-1.019), p=0.006] were associated with a reduced incidence of EOP. In addition, the pathogens detected by mNGS within 48 hours after ECPR were mainly oral colonizing bacteria and viruses, and viruses were in the majority, while all BALF cultures were negative. In contrast, between 48 hours and 7 days after ECPR, BALF cultures were positive in all EOP patients.<br><br>CONCLUSIONS: Early mNGS testing to identify microbial flora facilitates timely adjustment of antibiotic regimens, thereby reducing the incidence of EOP and improving short-term prognosis in patients undergoing ECPR following IHCA.},
}
@article {pmid39582659,
year = {2024},
author = {Chen, X and Yan, F and Qu, D and Wan, T and Xi, L and Hu, CY},
title = {Aroma characterization of Sichuan and Cantonese sausages using electronic nose, gas chromatography-mass spectrometry, gas chromatography-olfactometry, odor activity values and metagenomic.},
journal = {Food chemistry: X},
volume = {24},
number = {},
pages = {101924},
pmid = {39582659},
issn = {2590-1575},
abstract = {The interest of Chinese consumers in meat-free sausages has increased considerably due to their health benefits, but the aroma quality is far from reaching the traditional fermented meat sausages. This study evaluated the aroma characterization of Sichuan and Cantonese sausages using electronic nose (E-nose), gas chromatography-mass spectrometry (GC-MS), gas chromatography-olfactometry (GC-O), odor activity values (OAVs) and metagenomic. Ninety-eight volatile compounds were identified. Among them, 23 odorants were perceived, and their intensity differed in the two groups of sausages. There was a significant difference in the volatile compound profile between Sichuan and Cantonese cooked sausages. E-nose sensors could differentiate them through specific responses to these volatile compounds. Furthermore, there was a significant difference in microbial communities between Sichuan and Cantonese sausages. For aroma quality improvement of meat-free sausages, studies should focus on controlling the formation of aroma compounds by aroma precursors and using different microorganisms to produce diverse meat aromas. Our results provide a reference for the implementation of these strategies.},
}
@article {pmid39582622,
year = {2024},
author = {Nie, M and Yue, G and Wang, L and Zhang, Y},
title = {Short-term organic fertilizer substitution increases sorghum yield by improving soil physicochemical characteristics and regulating microbial community structure.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1492797},
pmid = {39582622},
issn = {1664-462X},
abstract = {INTRODUCTION: Chemical fertilizer reduction combined with organic fertilizer (organic fertilizer substitution) has a positive impact on crop productivity and sustainable development. However, the effects of short-term organic fertilizer substitution on microbial community structure and functions of sorghum rhizosphere soil and on sorghum yield remain unclear. Herein, this study investigated the short-term effects of organic fertilizer substitution on sorghum soil physicochemical properties, microbial community structure and enzyme activities using Metagenomic sequencing technology.<br><br>METHODS: The fertilization treatment included no fertilization (CK), pure chemical fertilizer N (CF), substitution of 25% chemical fertilizer N with organic N (NF25), substitution of 50% chemical fertilizer N with organic N (NF50), substitution of 75% chemical fertilizer N with organic N (NF75), and pure organic fertilizer N (NF100); soil samples were collected and analyzed in the flowering period of sorghum.<br><br>RESULTS AND DISCUSSION: The results showed that the suitable organic fertilizer substitution rate of sorghum field was 50%, and its yield was the highest among all treatments (9789.9 kg/hm[2]). Compared with the CF treatment, a medium ratio (50%) of organic fertilizer substitution significantly reduced soil alkalization (by 3.05%), improved soil nutrients, enhanced soil enzyme activities, and increased sorghum yield (P < 0.05). After organic fertilizer substitution treatment, higher protein, fat, and total starch levels accumulated in sorghum grains, and the tannin content of grains decreased. The effect of organic fertilizer substitution on bacterial diversity was greater than that on fungal diversity. Among the dominant bacterial phyla, the medium ratio of organic substitution treatment significantly increased the relative abundances of Proteobacteria (by 3.57%) and Actinomycetes (by 14.94%), and decreased the relative abundances of Acidobacteria (by 5.18%) and Planctomycetes (by 7.76%) compared with no fertilization, while the dominant fungal phyla did not respond significantly to the addition of organic fertilizer. Organic fertilizer substitution also improved soil microbial metabolic pathways, biosynthesis of secondary metabolites, and carbon metabolism. The biomarkers enriched in inorganic fertilizer treatment and organic fertilizer substitution treatments had similar relevant environmental elements but reversed correlation trends. Moreover, soil Alkali-hydrolyzable nitrogen and L-leucine aminopeptidase were important environmental factors influencing the structure of bacterial and fungal communities in sorghum soils, respectively. Soil nutrient levels and microbial communities together explained the variation in annual sorghum yield. The results of this study provide evidence that short-term organic fertilizer substitution increases sorghum yield by improving soil properties and regulating microbial community structure.},
}
@article {pmid39582241,
year = {2024},
author = {Zhang, M and Zhang, L and Suo, B and Wei, Y and Xu, Y and Jiang, M and Dong, J and Li, X and Song, Z and Liu, D},
title = {Distribution Characteristics and Impacting Factors of Drug CYP Enzymes and Transporters in the Gastrointestinal Tract of Chinese Healthy Subjects.},
journal = {Clinical pharmacology and therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1002/cpt.3497},
pmid = {39582241},
issn = {1532-6535},
abstract = {The abundance of drug metabolic enzymes (DMEs) and transporters (DTs) in the human gastrointestinal tract significantly affects xenobiotic exposure in the circulating system, the basis of these compounds acting on humans. However, accurately predicting individual exposure in healthy subjects remains challenging due to limited data on protein levels throughout the gastrointestinal tract within the same individuals and inadequate assessment of factors influencing these levels. Therefore, we conducted a clinical study to obtain biopsy samples from 8 different gastrointestinal segments in 24 healthy Chinese volunteers. Concurrently, blood and fecal samples were collected for genotypic analysis and fecal microbiota metagenomic sequencing. Using an optimized LC-MS/MS method, we quantified the absolute protein abundance of CYP2C9, CYP2C19, CYP2D6, CYP3A4, P-gp, and BCRP from the stomach to the colon. Our results revealed significant regional differences in protein expression: CYP3A4 was the most abundant in the small intestine, whereas CYP2C9 was predominantly found in the colon. CYP2D6 was primarily located in the ileum, while other DMEs/DTs showed higher concentrations in the jejunum. Meanwhile, the enzyme abundance in the small intestine and colon and the relative ratio of transporters in different regions to the jejunum were accurately calculated, providing valuable data for refining the physiological parameters in the virtual gastrointestinal tract of Chinese healthy population in PBBMs. Additionally, BMI, IBW, sex, age, genotype, and fecal microbiota were identified as critical factors influencing the protein levels of these DMEs/DTs throughout the gastrointestinal tract, with notable regional differences. Consequently, this study provides a unique foundation for understanding xenobiotic absorption in humans.},
}
@article {pmid39582065,
year = {2024},
author = {Velsko, IM and Fagernäs, Z and Tromp, M and Bedford, S and Buckley, HR and Clark, G and Dudgeon, J and Flexner, J and Galipaud, JC and Kinaston, R and Lewis, CM and Matisoo-Smith, E and Nägele, K and Ozga, AT and Posth, C and Rohrlach, AB and Shing, R and Simanjuntak, T and Spriggs, M and Tamarii, A and Valentin, F and Willie, E and Warinner, C},
title = {Exploring the potential of dental calculus to shed light on past human migrations in Oceania.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {10191},
pmid = {39582065},
issn = {2041-1723},
support = {EXC 2051, 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SRC 8038-06//National Geographic Society/ ; },
mesh = {Humans ; *Human Migration/history ; *Dental Calculus/microbiology/history ; Oceania ; *Microbiota/genetics ; Archaeology ; Phylogeny ; Pacific Islands ; Asia, Southeastern ; Metagenomics/methods ; DNA, Ancient/analysis ; History, Ancient ; Bacteria/genetics/classification/isolation &amp; purification ; },
abstract = {The Pacific islands and Island Southeast Asia have experienced multiple waves of human migrations, providing a case study for exploring the potential of ancient microbiomes to study human migration. We perform a metagenomic study of archaeological dental calculus from 102 individuals, originating from 10 Pacific islands and 1 island in Island Southeast Asia spanning ~3000 years. Oral microbiome DNA preservation in calculus is far higher than that of human DNA in archaeological bone, and comparable to that of calculus from temperate regions. Oral microbial community composition is minimally driven by time period and geography in Pacific and Island Southeast Asia calculus, but is found to be distinctive compared to calculus from Europe, Africa, and Asia. Phylogenies of individual bacterial species in Pacific and Island Southeast Asia calculus reflect geography. Archaeological dental calculus shows good preservation in tropical regions and the potential to yield information about past human migrations, complementing studies of the human genome.},
}
@article {pmid39581874,
year = {2024},
author = {Li, Y and Pan, G and Wang, S and Li, Z and Yang, R and Jiang, Y and Chen, Y and Li, SC and Shen, B},
title = {Comprehensive human respiratory genome catalogue underlies the high resolution and precision of the respiratory microbiome.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
doi = {10.1093/bib/bbae620},
pmid = {39581874},
issn = {1477-4054},
mesh = {Humans ; *Microbiota/genetics ; Genome, Human ; Metagenome ; Respiratory System/microbiology ; Bacteria/genetics/classification ; },
abstract = {The human respiratory microbiome plays a crucial role in respiratory health, but there is no comprehensive respiratory genome catalogue (RGC) for studying the microbiome. In this study, we collected whole-metagenome shotgun sequencing data from 4067 samples and sequenced long reads of 124 samples, yielding 9.08 and 0.42 Tbp of short- and long-read data, respectively. By submitting these data with a novel assembly algorithm, we obtained a comprehensive human RGC. This high-quality RGC contains 190,443 contigs over 1 kbps and an N50 length exceeding 13 kbps; it comprises 159 high-quality and 393 medium-quality genomes, including 117 previously uncharacterized respiratory bacteria. Moreover, the RGC contains 209 respiratory-specific species not captured by the unified human gastrointestinal genome. Using the RGC, we revisited a study on a pediatric pneumonia dataset and identified 17 pneumonia-specific respiratory pathogens, reversing an inaccurate etiological conclusion due to the previous incomplete reference. Furthermore, we applied the RGC to the data of 62 participants with a clinical diagnosis of infection. Compared to the Nucleotide database, the RGC yielded greater specificity (0 versus 0.444, respectively) and sensitivity (0.852 versus 0.881, respectively), suggesting that the RGC provides superior sensitivity and specificity for the clinical diagnosis of respiratory diseases.},
}
@article {pmid39581825,
year = {2024},
author = {Isali, I and Almassi, N and Nizam, A and Campbell, R and Weight, C and Gupta, S and Pooja, G and Fulmes, A and Mishra, K and Abbosh, P and Bukavina, L},
title = {State of the Art: The Microbiome in Bladder Cancer.},
journal = {Urologic oncology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.urolonc.2024.11.008},
pmid = {39581825},
issn = {1873-2496},
abstract = {This review assesses the current understanding of the relationship between the human microbiome and BCa. Recognizing how the microbiome affects the tumor microenvironment provides valuable insights into cancer biology, potentially uncovering interactions that could be leveraged to develop innovative therapeutic approaches. By clarifying these intricate microbial-tumor dynamics, novel targets for microbiome-based interventions can be identified, ultimately improving treatment effectiveness and patient outcomes. Current literature lacks comprehensive insights into the effects of BCa treatment on the microbiome and the prevalence of immunotherapy-related toxicities. Further research into the microbiome's role in BCa development could bridge the gap between fundamental research and therapeutic applications. Implementing microbiome surveillance, metagenomic sequencing, and metabolomics in clinical trials could deepen our understanding of BCa and its treatment. This review explores the existing understanding of the urine, tissue, and gut microbiomes and their connections to BCa. Enhanced knowledge of these relationships can pave the way for future research to identify reliable disease predictors, prognostic markers, and novel therapeutic targets.},
}
@article {pmid39581538,
year = {2024},
author = {Olie, SE and Staal, SL and van de Beek, D and Brouwer, MC},
title = {Diagnosing infectious encephalitis: a Narrative review.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2024.11.026},
pmid = {39581538},
issn = {1469-0691},
abstract = {BACKGROUND: Diagnosing infectious encephalitis can be challenging as it can be caused by a wide range of pathogens, with viruses being the most common cause. In a substantial number of patients, no pathogen is identified despite a clinical diagnosis of infectious encephalitis. Recent advancements in diagnostic testing have introduced new methods to address this diagnostic challenge and improve pathogen detection.<br><br>OBJECTIVES: To provide a comprehensive clinical approach for diagnosing infectious encephalitis and explore novel diagnostic methods.<br><br>SOURCES: We searched PubMed to identify relevant literature on diagnosing encephalitis in English up to the September 1[st] 2024as well as included articles known by the authors.<br><br>CONTENT: Clinical characteristics may suggest a specific cause of infectious encephalitis, but are insufficient to guide treatment decisions. Therefore, cerebrospinal fluid (CSF) examination remains the cornerstone of the diagnostic process, with CSF leukocyte count being the most reliable predictor for central nervous system (CNS) infections. CSF features can be normal, however, in a proportion of patients presenting with infectious encephalitis. A definite diagnosis of infectious encephalitis is established by microbiological or histopathological tests in approximately 50% of patients. Additional investigations, including neuroimaging or EEG, can provide evidence for encephalitis or help to identify alternate conditions, although their role is primarily supportive. Emerging diagnostic techniques, including next generation sequencing metagenomics and unbiased serology (PhipSeq), have the potential to increase the proportion of patients with a confirmed diagnosis. However, these techniques are not yet practical due to their complex analysis, long turnaround times and high costs.<br><br>IMPLICATIONS: Microbiological confirmation is paramount in the diagnosis of infectious encephalitis, but it is currently established in about half of cases. While novel techniques show promise to increase the proportion of cause specific diagnoses, they are not yet suitable for routine use. This highlights the ongoing need for advancements in diagnostic methods.},
}
@article {pmid39581260,
year = {2024},
author = {Lee, YH and Park, HJ and Jeong, SJ and Auh, QS and Jung, J and Lee, GJ and Shin, S and Hong, JY},
title = {Oral microbiome profiles of gingivitis and periodontitis by next-generation sequencing among a group of hospital patients in Korea: A cross-sectional study.},
journal = {Journal of oral biosciences},
volume = {},
number = {},
pages = {100591},
doi = {10.1016/j.job.2024.100591},
pmid = {39581260},
issn = {1880-3865},
abstract = {OBJECTIVES: The oral microbiome plays an important role in the development and progression of periodontal disease. The purpose of this study was to compare microbial profiles of oral cavities in good health, with gingivitis, and in a state of periodontitis, and to identify novel pathogens involved in periodontal diseases.<br><br>METHODS: One hundred and two participants, including 33 healthy controls, 41 patients with gingivitis, and 28 patients with periodontitis, were included in this cross-sectional study. Salivary oral microbiomes were investigated using 16S rRNA metagenomic sequencing, and the microbial profiles of each group were compared using age- and sex-adjusted general linear models.<br><br>RESULTS: The abundance of amplicon sequence variants and Chao1 diversity were significantly elevated in the gingivitis and periodontitis groups relative to healthy controls (p = 0.046). Based on linear discriminant analysis (LDA) scores (>2), Tenericutes, Mollicutes, Mycoplasmatales, Mycoplasmataceae, Mycoplasma, Bacteroidaceae, and Phocaeicola were significantly enriched in the gingivitis group, and Synergistetes, Synergistia, Synergistales, Synergistaceae, Fretibacterium, Sinanaerobacter, and Filifactor were enriched in the periodontitis group. The relative abundances of Fretibacterium fastidiosum, Sinanaerobacter chloroacetimidivorans, and Filifactor alocis (q = 0.008, all bacteria) were highest in the periodontitis group and lowest in the control group. The relative abundance of Treponema denticola was significantly elevated in the periodontitis group compared to the other two groups (q = 0.024).<br><br>CONCLUSIONS: Oral microbiomes differed between groups. T. denticola, F. fastidiosum, S. chloroacetimidivorans and F. alocis were significantly more abundant in the periodontitis group than in the control group. Additionally, the abundance of T. denticola and F. fastidiosum in the periodontitis group was significantly different from that in the gingivitis group.},
}
@article {pmid39580945,
year = {2024},
author = {Su, Y and Feng, L and Duan, X and Peng, H and Zhao, Y and Chen, Y},
title = {Deciphering the function of Fe3O4 in alleviating propionate inhibition during high-solids anaerobic digestion: Insights of physiological response and energy conservation.},
journal = {Water research},
volume = {270},
number = {},
pages = {122811},
doi = {10.1016/j.watres.2024.122811},
pmid = {39580945},
issn = {1879-2448},
abstract = {Fe3O4 is a recognized addictive to enhance low solid anaerobic digestion (AD), while for high solid AD challenged by acidity inhibition, its feasibility and mechanism remain unclear. In this study, the positive effect of Fe3O4 on high-solids AD of food waste by regulating microbial physiology and energy conservation to enhance mutualistic propionate methanation was documented. The methane yield was increased by 36.7 % with Fe3O4, which because Fe3O4 alleviated propionate stress on methane generation, along with improved propionate degradation and methanogenic metabolism. Fe3O4 facilitated the production of extracellular polymeric substances and the formation of tightly bio-aggregates, fostering an enriched microbial population (e.g., Smithella and Methanosaeta) to resist propionate stress. Also, Fe3O4 up-regulated the genes in stress defense system, cytomembrane biosynthesis/function, metal irons transporter, cell division and enzyme synthesis, verifying its superiority on cellular physiology. In addition, energy-conservation strategies related to intracellular and extracellular electron transfer were enhanced by Fe3O4. Specifically, the enzyme expressions involved in reversed electron transfer and electron bifurcation coupled with direct interspecies electron transfer (DIET) were upregulated by at least 2.2 times with Fe3O4, providing sufficient energy to drive thermodynamic adverse methanogenesis from propionate-stressed condition. Consequently, the reinforced enzyme expression in the dismutation and DIET pathway make it to be the predominant drivers for enhanced methanogenic propionate metabolism. This study fills the knowledge gaps of Fe3O4-induced microbial physiological and energetic strategies to resist environmental stress, and has remarkable practical implicated for restoring inhibited bioactivities.},
}
@article {pmid39580871,
year = {2024},
author = {Kumar, S and Bhatia, Z and Seshadri, S},
title = {Formulated chitosan microspheres remodelled the altered gut microbiota and liver miRNA in diet-induced Type-2 diabetic rats.},
journal = {Carbohydrate research},
volume = {547},
number = {},
pages = {109301},
doi = {10.1016/j.carres.2024.109301},
pmid = {39580871},
issn = {1873-426X},
abstract = {Chitosan was formulated into a microsphere and comprehensively characterized and evaluated for its anti-inflammatory potential and anti-diabetic properties against the high sugar fat diet-induced diabetic animals. The diabetic model was induced through feeding with a high-sugar fat diet. Metformin, a standard antidiabetic drug, and CMS (chitosan microspheres) were administered orally for 90 days as reversal strategies. Upon completion of the study, the following parameters, such as serum biochemistry, cytokine analysis, tissue histology, liver miRNA sequencing, and Shotgun metagenomics studies from stool samples, were performed. SEM images of the microsphere indicated a smooth morphology, while FTIR and DSC respectively, confirmed the presence of functional groups of chitosan and the thermal stability of the formulation. Following HSFD induction, all the parameters analyzed were altered compared to the control group. In both reversal groups, serum biochemical parameters were restored, which was at par with the control. A significant increase in the anti-inflammatory cytokine IL-10, and a remarkable reduction in TNF-α and MCP-1 inflammatory cytokines were observed in both reversal groups. Tissue histology indicated improvements in low-grade inflammation, induced in the diabetic group. miR-203 was upregulated in the CMS-treated group, while miR-103 was downregulated. The study further delved into the impact on gut microbiota and KEGG. Major phyla i.e., Bacteroidetes, Cyanobacteria, Firmicutes, Proteobacteria, and Verrucomicrobia showed restoration, while upregulation of DNA polymerase zeta in T2D showed reversal after the treatment. The formulation showed reversal at par with metformin and also confirms its anti-diabetic and anti-inflammatory activities of CMS, with microfloral and miR regulatory functions.},
}
@article {pmid39580566,
year = {2024},
author = {Gomes, WDS and Partelli, FL and Veloso, TGR and da Silva, MCS and Moreli, AP and Moreira, TR and Pereira, LL},
title = {Effects of Coffea canephora genotypes on the microbial community of soil and fruit.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {29035},
pmid = {39580566},
issn = {2045-2322},
support = {23186000886201801//Sul Serrana of Esp&#xed;rito Santo Free Admission Credit Cooperative- SICOOB/ ; 23186000886201801//Sul Serrana of Esp&#xed;rito Santo Free Admission Credit Cooperative- SICOOB/ ; 23186000886201801//Sul Serrana of Esp&#xed;rito Santo Free Admission Credit Cooperative- SICOOB/ ; },
mesh = {*Coffea/microbiology/genetics ; *Soil Microbiology ; *Fruit/microbiology ; *Genotype ; *Microbiota/genetics ; *Rhizosphere ; Bacteria/genetics/classification/isolation &amp; purification ; Fungi/genetics/classification/isolation &amp; purification ; Brazil ; Soil ; RNA, Ribosomal, 16S/genetics ; },
abstract = {In recent years, the role of microbial communities in agricultural systems has received increasing attention, particularly concerning their impact on plant health and productivity. However, the influence of host plant genetic factors on the microbial composition of coffee plants remains largely unexplored. This study provides the first comprehensive investigation into how genotype affects the microbial communities present in the rhizosphere and fruits of Coffea canephora. Conducted on a commercial coffee farm in Brazil, we analyzed six genotypes of C. canephora var. Conilon. Soil and fruit samples were collected from which microbial DNA was extracted and sequenced, targeting the V3-V4 region of the 16 S rDNA and the ITS1 region for fungi. A total of 12,239,769 reads were generated from the 16 S rDNA and ITS1 regions. The PCoA revealed distinct patterns of beta diversity, with genotype 153 exhibiting significant isolation in soil bacterial communities. The dominant bacterial orders included Rhizobiales and Rhodobacterales, while the fungal community comprised diverse taxa from Saccharomycetales and Hypocreales. LEfSe analysis identified key metagenomic biomarkers, highlighting genotype Baiano 4 for its richness in fruit-associated taxa, whereas genotype 153 exhibited lower diversity in both soil and fruit samples. This work enhances our understanding of the microbiomes associated with different coffee genotypes, providing evidence of how host genetic variation influences microbial community composition. Our findings indicate that specific microbial taxa are enriched in the fruits and soil of various genotypes. Future research should focus on identifying these microorganisms and elucidating their specific functions within the rhizosphere and coffee fruits.},
}
@article {pmid39580523,
year = {2024},
author = {Li, J and Zhai, X and Chen, C and Zhang, R and Huang, X and Liu, Y},
title = {The intrahepatic bacterial metataxonomic signature of patients with hepatocellular carcinoma.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {29077},
pmid = {39580523},
issn = {2045-2322},
support = {32300081//the National Natural Science Foundation of China/ ; 23QA1406600//Shanghai Science and Technology Committee/ ; },
mesh = {Humans ; *Carcinoma, Hepatocellular/microbiology/pathology/metabolism ; *Liver Neoplasms/microbiology/pathology/metabolism ; Male ; Female ; Middle Aged ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Aged ; Liver/microbiology/pathology/metabolism ; Microbiota ; Liver Cirrhosis/microbiology/pathology ; Adult ; },
abstract = {Dysbiosis of the gut-liver axis increases the risk of bacterial and metabolite influx into the liver, which may contribute to the development of hepatocellular carcinoma (HCC). In this study, we compared the microbiomes in HCC tumors and adjacent tissues. We examined the HCC tumors and adjacent tissues from 19 patients diagnosed with HCC. We find that the liver tissues from HCC patients with capsule invasion presented higher alpha diversity at the genus level than those without. The bacterial compositions in liver tissues of HCC patients at stage II differed from those at stage I and Advanced, respectively. Metagenomic profiling revealed that order Actinomycetales was enriched in the HCC patients at advanced stages. Order Lactobacillales, family Veillonellaceae, genera Rhodobacter and Megasphaera are enriched in tumors of HCC patients, whereas genus Pseudochrobactrum is enriched in the adjacent tissues from HCC patients. An increased abundance of class Actinobacteria and order Actinomycetales is observed in the HCC patients with cirrhosis. In contrast, phylum Firmicutes, classes Clostridia and Betaproteobacteria, and order Clostridiales are enriched in those without cirrhosis. The presence of various types of bacterial 16S rRNAs in HCC tumors and adjacent tissues indicates the presence of various bacterial communities therein. Our study provides information about differentially abundant intrahepatic bacteria in patients with HCC. The differences found may support possible diagnostic and personalized therapeutic implications for HCC.},
}
@article {pmid39579702,
year = {2024},
author = {Hou, J and Li, Y and Liu, M and Qu, Z and Du, Z and An, Y and Yang, F and Yao, Y},
title = {Significant effects of bioavailable heavy metals on antibiotic resistome in paddy soils as revealed by metagenomic analysis.},
journal = {Journal of hazardous materials},
volume = {482},
number = {},
pages = {136587},
doi = {10.1016/j.jhazmat.2024.136587},
pmid = {39579702},
issn = {1873-3336},
abstract = {Heavy metals (HMs) act as a long-term selective pressure for the emergence and maintenance of antibiotic resistance genes (ARGs) in agricultural soils. However, the effects of HMs on ARG distributions in paddy soils and the underlying mechanisms remain unclear. In this study, 74 soil samples were collected from the paddy fields to explore the impact of HMs on ARG profiles. A total of 468 ARGs were detected in HM-contaminated soils. Variation partitioning analysis (VPA) and redundancy analysis (RDA) demonstrated that the bioavailable HMs contributed more significantly to ARG composition compared to the total HM content (8.59 % vs. 3.97 %). Structural equation models (SEMs) showed that bioavailable HMs affected ARGs mainly by negatively altering the microbial diversity. Furthermore, the co-occurrence analysis of ARGs and metal resistant genes (MRGs) was further performed at the metagenome-assembled genomes (MAGs) level. Consequently, 1145 MAGs that assigned to 29 bacterial phyla were found to concurrently harbor ARGs and MRGs, with the bacterial phyla Pseudomonadota being predominant ARG-MRG-carrying microbes for most coexistence types of ARGs and MRGs, i.e., multidrug-As, polymyxin-Cd, Quinolone-Cd, Beta-lactam-Pb, and multidrug-Zn. Our findings highlight that the extensive coexistence of ARG-MRG in microbial genomes is an important reason for the ARG pollution in HM-contaminated paddy soils.},
}
@article {pmid39579692,
year = {2024},
author = {Hu, R and Chen, X and Han, Y and Li, W and Zhang, S and Liu, Z and Wang, J and Lu, X and Luo, G and Zhang, S and Zhen, G},
title = {KOH-modified biochar enhances nitrogen metabolism of the chloroquine phosphate-disturbed anammox: Physical binding, EPS modulation and versatile metabolic hierarchy.},
journal = {Journal of hazardous materials},
volume = {482},
number = {},
pages = {136467},
doi = {10.1016/j.jhazmat.2024.136467},
pmid = {39579692},
issn = {1873-3336},
abstract = {Chloroquine phosphate (CQ) poses strong biotoxicity on anammox process, and thus detoxifying is essential for the stable operation of anammox in treating CQ-bearing wastewater. Biochar has been proven to simultaneously detoxify pollutant and modulate nitrogen cycle in anammox by its shelter effect and electron exchange capacity (EEC) ability. To further improve the ability of biochar to promote the nitrogen metabolism of anammox, a KOH modification strategy was used to tailor a high-EEC biochar in this work. KOH modified biochar can bind CQ for detoxification driven by hydrogen bond, π-π interaction, and electrostatic interaction. Meanwhile, the EEC of modified biochar increased by 70 % than that of pristine biochar, thus improving nitrogen removal efficiency by 55.6 % and 9.5 % than CQ and BC group, respectively. Besides, the microorganism regulated by modified biochar produced more α-helix configuration, improving EPS barrier ability to CQ and sludge granulation. Lastly, metagenomic analysis revealed that modified biochar can stimulate the Wood-Ljungdahl pathway, increased the relative abundance of CODH from 0.74 % in CQ to 1.00 % in modified BC group. It favored the proliferation of autotrophic microorganisms, especially increased the relative abundance of anammox bacteria by 86.8 % than CQ group. This work will shed the light on integrating high-EEC biochar into anammox to cope with the micropollutants stress.},
}
@article {pmid39579348,
year = {2024},
author = {Ramos-Barbero, MD and Aldeguer-Riquelme, B and Viver, T and Villamor, J and Carrillo-Bautista, M and López-Pascual, C and Konstantinidis, KT and Martínez-García, M and Santos, F and Rossello-Mora, R and Antón, J},
title = {Experimental evolution at ecological scales allows linking of viral genotypes to specific host strains.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae208},
pmid = {39579348},
issn = {1751-7370},
abstract = {Viruses shape microbial community structure and activity through the control of population diversity and cell abundances. Identifying and monitoring the dynamics of specific virus-host pairs in nature is hampered by the limitations of culture-independent approaches such as metagenomics, which do not always provide strain-level resolution, and culture-based analyses, which eliminate the ecological background and in-situ interactions. Here, we have explored the interaction of a specific "autochthonous" host strain and its viruses within a natural community. Bacterium Salinibacter ruber strain M8 was spiked into its environment of isolation, a crystallizer pond from a coastal saltern, and the viral and cellular communities were monitored for one month using culture, metagenomics, and microscopy. Metagenome sequencing indicated that the M8 abundance decreased sharply after being added to the pond, likely due to forces other than viral predation. However, the presence of M8 selected for two species of a new viral genus, Phoenicisalinivirus, for which 120 strains were isolated. During this experiment, an assemblage of closely related viral genomic variants was replaced by a single population with the ability to infect M8, a scenario which was compatible with the selection of a genomic variant from the rare biosphere. Further analysis implicated a viral genomic region putatively coding for a tail fiber protein to be responsible for M8 specificity. Our results indicate that low abundance viral genotypes provide a viral seed bank that allows for a highly specialized virus-host response within a complex ecological background.},
}
@article {pmid39579086,
year = {2024},
author = {Peng, C and Shang, J and Guan, J and Wang, D and Sun, Y},
title = {ViraLM: Empowering Virus Discovery through the Genome Foundation Model.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btae704},
pmid = {39579086},
issn = {1367-4811},
abstract = {MOTIVATION: Viruses, with their ubiquitous presence and high diversity, play pivotal roles in ecological systems and public health. Accurate identification of viruses in various ecosystems is essential for comprehending their variety and assessing their ecological influence. Metagenomic sequencing has become a major strategy to survey the viruses in various ecosystems. However, accurate and comprehensive virus detection in metagenomic data remains difficult. Limited reference sequences prevent alignment-based methods from identifying novel viruses. Machine learning-based tools are more promising in novel virus detection but often miss short viral contigs, which are abundant in typical metagenomic data. The inconsistency in virus search results produced by available tools further highlights the urgent need for a more robust tool for virus identification.<br><br>RESULTS: In this work, we develop ViraLM for identifying novel viral contigs in metagenomic data. By employing the latest genome foundation model as the backbone and training on a rigorously constructed dataset, the model is able to distinguish viruses from other organisms based on the learned genomic characteristics. We thoroughly tested ViraLM on multiple datasets and the experimental results show that ViraLM outperforms available tools in different scenarios. In particular, ViraLM improves the F1-score on short contigs by 22%.<br><br>AVAILABILITY: The source code of ViraLM is available via: https://github.com/ChengPENG-wolf/ViraLM.},
}
@article {pmid39578925,
year = {2024},
author = {Geers, AU and Buijs, Y and Schostag, MD and Elberling, B and Bentzon-Tilia, M},
title = {Exploring the biosynthesis potential of permafrost microbiomes.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {96},
pmid = {39578925},
issn = {2524-6372},
support = {DNRF 100//Danmarks Grundforskningsfond/ ; DNRF 137//Danmarks Grundforskningsfond/ ; DFF - 8048-00035B//Danmarks Frie Forskningsfond/ ; NNF21OC0070749//Novo Nordisk Fonden/ ; },
abstract = {BACKGROUND: Permafrost microbiomes are of paramount importance for the biogeochemistry of high latitude soils and while endemic biosynthetic domain sequences involved in secondary metabolism have been found in polar surface soils, the biosynthetic potential of permafrost microbiomes remains unexplored. Moreover, the nature of these ecosystems facilitates the unique opportunity to study the distribution and diversity of biosynthetic genes in relic DNA from ancient microbiomes. To explore the biosynthesis potential in permafrost, we used adenylation (AD) domain sequencing to evaluate non-ribosomal peptide (NRP) production in permafrost cores housing microbiomes separated at kilometer and kiloyear scales.<br><br>RESULTS: Permafrost microbiomes represented NRP repertoires significantly different from that of temperate soil microbiomes, but as for temperate soils, the estimated domain richness and diversity was strongly correlated to the bacterial taxonomic diversity across locations. Furthermore, we found significant differences in both community composition and AD domain composition across geographical and temporal distances. Overall, the vast majority of biosynthetic domains showed below 90% amino acid similarity to characterized BGCs, confirming the high degree of novelty of NRPs inherent to permafrost microbiomes. Using available metagenomic sequences, we further identified a high biosynthetic diversity beyond NRPs throughout arctic surface soils down to deep and ancient (megayear old) permafrost microbiomes.<br><br>CONCLUSION: We have shown that arctic permafrost microbiomes harbor a unique biosynthetic repertoire rich in hitherto undescribed NRPs. This diversity is driven by geographic separation across kilometer scales and by the bacterial taxonomic diversity between microbiomes confined in separate permafrost layers. Hence the permafrost biome represents a unique resource for studying secondary metabolism, and potentially for the discovery of novel drug leads.},
}
@article {pmid39578870,
year = {2024},
author = {Wang, Y and Chen, X and Huws, SA and Xu, G and Li, J and Ren, J and Xu, J and Guan, LL and Yao, J and Wu, S},
title = {Ileal microbial microbiome and its secondary bile acids modulate susceptibility to nonalcoholic steatohepatitis in dairy goats.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {247},
pmid = {39578870},
issn = {2049-2618},
mesh = {Animals ; *Non-alcoholic Fatty Liver Disease/microbiology ; *Goats ; *Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome ; *Ileum/microbiology ; *Liver/metabolism ; Mice ; Bacteria/classification/isolation &amp; purification/genetics ; Disease Susceptibility ; Goat Diseases/microbiology ; Disease Models, Animal ; Female ; },
abstract = {BACKGROUND: Liver damage from nonalcoholic steatohepatitis (NASH) presents a significant challenge to the health and productivity of ruminants. However, the regulatory mechanisms behind variations in NASH susceptibility remain unclear. The gut‒liver axis, particularly the enterohepatic circulation of bile acids (BAs), plays a crucial role in regulating the liver diseases. Since the ileum is the primary site for BAs reabsorption and return to the liver, we analysed the ileal metagenome and metabolome, liver and serum metabolome, and liver single-nuclei transcriptome of NASH-resistant and susceptible goats together with a mice validation model to explore how ileal microbial BAs metabolism affects liver metabolism and immunity, uncovering the key mechanisms behind varied NASH pathogenesis in dairy goats.<br><br>RESULTS: In NASH goats, increased total cholesterol (TC), triglyceride (TG), and primary BAs and decreased secondary BAs in the liver and serum promoted hepatic fat accumulation. Increased ileal Escherichia coli, Erysipelotrichaceae bacterium and Streptococcus pneumoniae as well as proinflammatory compounds damaged ileal histological morphology, and increased ileal permeability contributes to liver inflammation. In NASH-tolerance (NASH-T) goats, increased ursodeoxycholic acid (UDCA), isodeoxycholic acid (isoDCA) and isolithocholic acid (isoLCA) in the liver, serum and ileal contents were attributed to ileal secondary BAs-producing bacteria (Clostridium, Bifidobacterium and Lactobacillus) and key microbial genes encoding enzymes. Meanwhile, decreased T-helper 17 (TH17) cells and increased regulatory T (Treg) cells proportion were identified in both liver and ileum of NASH-T goats. To further validate whether these key BAs affected the progression of NASH by regulating the proliferation of TH17 and Treg cells, the oral administration of bacterial UDCA, isoDCA and isoLCA to a high-fat diet-induced NASH mouse model confirmed the amelioration of NASH through the TH17 cell differentiation/IL-17 signalling/PPAR signalling pathway by these bacterial secondary BAs.<br><br>CONCLUSION: This study revealed the roles of ileal microbiome and its secondary BAs in resilience and susceptibility to NASH by affecting the hepatic Treg and TH17 cells proportion in dairy goats. Bacterial UDCA, isoDCA and isoLCA were demonstrated to alleviate NASH and could be novel postbiotics to modulate and improve the liver health in ruminants. Video Abstract.},
}
@article {pmid39578769,
year = {2024},
author = {Deng, H and Shi, Y and Xie, M and Zang, X and Zang, X and Ma, X and Han, W and He, J and Rao, Y and Ding, M and Ma, W and Wu, J and Pan, L and Xue, X},
title = {Diagnosis and treatment experience of Chlamydia psittaci pneumonia: A multicenter retrospective study in China.},
journal = {BMC infectious diseases},
volume = {24},
number = {1},
pages = {1333},
pmid = {39578769},
issn = {1471-2334},
support = {2021YFC2302100//National Key R&amp;D Program of China/ ; 2021YFC2302100//National Key R&amp;D Program of China/ ; 2023DTRXXY//Beijing Shijtan Hospital's "14th Five-Year Plan" Talent Cultivation Project/ ; 2023DTRXXY//Beijing Shijtan Hospital's "14th Five-Year Plan" Talent Cultivation Project/ ; },
mesh = {Humans ; Retrospective Studies ; Male ; China/epidemiology ; Female ; *Chlamydophila psittaci/isolation &amp; purification ; Middle Aged ; *Psittacosis/diagnosis/drug therapy/microbiology ; Adult ; *Anti-Bacterial Agents/therapeutic use ; Aged ; C-Reactive Protein/analysis ; Chlamydial Pneumonia/diagnosis/drug therapy/microbiology ; },
abstract = {BACKGROUND: In recent years, clinical cases of Chlamydia psittaci pneumonia have gradually increased. Chlamydia psittaci pneumonia can quickly progress to severe pneumonia, leading to respiratory failure. Chlamydia psittaci cannot be detected by commonly used detection methods, leading to difficulties in clinical diagnosis and treatment, which may eventually develop into severe Chlamydia psittaci pneumonia. Therefore, we should improve our diagnostic and treatment capabilities for this disease.<br><br>METHODS: This article retrospectively studied 61 cases of pneumonia from 12 different provinces in China, and classified them into severe pneumonia and non-severe pneumonia. Divided into two groups, with 23 cases of severe pneumonia and 38 cases of non-severe pneumonia. We compared the two groups in terms of imaging, laboratory testing, treatment, prognosis, etc., hoping to provide better explanations and help clinical physicians better diagnose the disease.<br><br>RESULTS: There is no difference in age, gender, contact history, smoking history, or basic disease between severe and non-severe Chlamydia psittaci pneumonia. The most prominent symptom is fever, with a median body temperature of 39.7 &#x2103;, and other symptoms similar to common respiratory infections. White blood cells and neutrophils may not show significant elevation, but C-reactive protein (CRP) and procalcitonin (PCT) will both show significant elevation, often accompanied by a decrease in arterial oxygen pressure. Some patients may experience liver and kidney dysfunction, but there is no statistically significant difference between the two groups. Doxycycline remains the preferred drug for severe Chlamydia psittaci pneumonia. The imaging mainly shows consolidation and bronchial inflation sign, and may also present with pleural effusion.<br><br>CONCLUSIONS: The imaging of Chlamydia psittaci pneumonia usually shows consolidation with bronchial inflation sign, which can also be manifested as ground glass changes or solid masses. Atypical images are prone to misdiagnosis in the early stages. There are some differences in laboratory examination and imaging between severe pneumonia and non-severe pneumonia, which can help identify severe patients in the early stage. Metagenomic next-generation sequencing (mNGS) played an important role in the diagnosis of all cases in this article. Timely treatment has a good prognosis for the disease, and imaging lesions can be completely absorbed.},
}
@article {pmid39578630,
year = {2024},
author = {Barber, DG and Child, HT and Joslin, GR and Wierzbicki, L and Tennant, RK},
title = {Statistical design approach enables optimised mechanical lysis for enhanced long-read soil metagenomics.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {28934},
pmid = {39578630},
issn = {2045-2322},
support = {CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; },
mesh = {*Metagenomics/methods ; *Soil Microbiology ; Soil/chemistry ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; },
abstract = {Metagenomic analysis has enabled insights into soil community structure and dynamics. Long-read sequencing for metagenomics can enhance microbial ecology by improving taxonomic classification, genome assembly, and functional annotation. However, protocols for purifying high-molecular weight DNA from soil are not yet optimised. We used a statistical design of experiments approach to enhance mechanical lysis of soil samples, increasing the length of purified DNA fragments. Low energy input into mechanical lysis improved DNA integrity, resulting in longer sequenced reads. Our optimized settings of 4 m s[-1] for 10 s increased fragment length by 70% compared to the manufacturer's recommendations. Longer reads from low intensity lysis produced longer contiguous sequences after assembly, potentially improving a range of down-stream analyses. Importantly, there was minimal bias exhibited in the microbial community composition due to lysis efficiency variations. We therefore propose a framework for improving the fragment lengths of DNA purified from diverse soil types, improving soil science research with long-read sequencing.},
}
@article {pmid39578464,
year = {2024},
author = {Nunn, BL and Timmins-Schiffman, E and Mudge, MC and Plubell, DL and Chebli, G and Kubanek, J and Riffle, M and Noble, WS and Harvey, E and Nunn, TA and Huntemann, M and Clum, A and Foster, B and Foster, B and Roux, S and Palaniappan, K and Mukherjee, S and Reddy, TBK and Daum, C and Copeland, A and Chen, IA and Ivanova, NN and Kyrpides, NC and Glavina Del Rio, T and Eloe-Fadrosh, EA},
title = {Microbial Metagenomes Across a Complete Phytoplankton Bloom Cycle: High-Resolution Sampling Every 4 Hours Over 22 Days.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1270},
pmid = {39578464},
issn = {2052-4463},
support = {R21ES034337-01//U.S. Department of Health &amp; Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; R21ES034337-01//U.S. Department of Health &amp; Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; R21ES034337-01//U.S. Department of Health &amp; Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; R21ES034337-01//U.S. Department of Health &amp; Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; R21ES034337-01//U.S. Department of Health &amp; Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; R21ES034337-01//U.S. Department of Health &amp; Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; R21ES034337-01//U.S. Department of Health &amp; Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; R21ES034337-01//U.S. Department of Health &amp; Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; 2041497//NSF | BIO | Division of Integrative Organismal Systems (IOS)/ ; IOS 2041497//NSF | BIO | Division of Integrative Organismal Systems (IOS)/ ; IOS 2041497//NSF | BIO | Division of Integrative Organismal Systems (IOS)/ ; IOS 2041497//NSF | BIO | Division of Integrative Organismal Systems (IOS)/ ; },
mesh = {*Phytoplankton/genetics/growth &amp; development ; *Metagenome ; *Bacteria/genetics/growth &amp; development/classification ; *Archaea/genetics ; Eutrophication ; Microbiota ; Viruses/genetics/growth &amp; development ; },
abstract = {In May and June of 2021, marine microbial samples were collected for DNA sequencing in East Sound, WA, USA every 4 hours for 22 days. This high temporal resolution sampling effort captured the last 3 days of a Rhizosolenia sp. bloom, the initiation and complete bloom cycle of Chaetoceros socialis (8 days), and the following bacterial bloom (2 days). Metagenomes were completed on the time series, and the dataset includes 128 size-fractionated microbial samples (0.22-1.2 µm), providing gene abundances for the dominant members of bacteria, archaea, and viruses. This dataset also has time-matched nutrient analyses, flow cytometry data, and physical parameters of the environment at a single point of sampling within a coastal ecosystem that experiences regular bloom events, facilitating a range of modeling efforts that can be leveraged to understand microbial community structure and their influences on the growth, maintenance, and senescence of phytoplankton blooms.},
}
@article {pmid39577783,
year = {2024},
author = {Calisto, R and Godinho, O and Devos, D and Lage, OM},
title = {"Genome-based in silico assessment of biosynthetic gene clusters in Planctomycetota: Evidences of its wide divergent nature".},
journal = {Genomics},
volume = {},
number = {},
pages = {110965},
doi = {10.1016/j.ygeno.2024.110965},
pmid = {39577783},
issn = {1089-8646},
abstract = {The biotechnological potential of Planctomycetota only recently started to be unveiled. 129 reference genomes and 5194 available genomes (4988 metagenome-assembled genomes (MAGs)) were analysed regarding the presence of Biosynthetic Gene Clusters (BGCs). By antiSMASH, 987 BGCs in the reference genomes and 22,841 BGCs in all the available genomes were detected. The classes Ca Uabimicrobiia, Ca Brocadiia and Planctomycetia had the higher number of BGC per genome, while Phycisphaerae had the lowest number. The most prevalent BGCs found in Planctomycetota reference genomes were terpenes, NRPS, type III PKS, type I PKS. As much as 88 % of the predicted regions had no similarity with known clusters in MIBiG database. This study strengthens the uniqueness of Planctomycetota for the isolation of new compounds and provide an overview of BGCs taxonomic distribution and of the type of predicted product. This outline allows the acceleration and focus of the research on drug discovery in Planctomycetota.},
}
@article {pmid39577779,
year = {2024},
author = {Wang, Y and Wei, W and Yang, D and Wu, L and Chen, X and Dai, X and Ni, BJ},
title = {Unraveling temperature effects on caproate and caprylate production from waste activated sludge.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131844},
doi = {10.1016/j.biortech.2024.131844},
pmid = {39577779},
issn = {1873-2976},
abstract = {This study explored the impact of different temperatures on the continuous production of medium-chain fatty acids (MCFAs) from waste activated sludge (WAS). Experimental results showed that there was almost no MCFAs accumulation at 55 °C. Both 25 °C and 37 °C were suitable for MCFAs production, with 25 °C favoring high-value caprylate production. The metagenomic and metatranscriptomic analysis highlighted reverse β-oxidization as the main chain elongation (CE) cycle. The lack of CE-related microorganisms and enzymes at 55 °C hindered MCFAs production, in contrast to the heightened activity observed at 25 °C and 37 °C, with peak activity at 25 °C leading to increased longer-chain MCFAs synthesis. 37 °C promoted hydrolysis and acidification, resulting in a accumulation of higher short-chain fatty acids, but further elongation to MCFAs would be hindered by product toxicity. This research concludes that 25 °C is the most effective temperature for the production of WAS-derived MCFAs, offering significant economic advantages.},
}
@article {pmid39577778,
year = {2024},
author = {Chen, Y and Huang, M and Fu, Y and Gao, T and Gan, Z and Meng, F},
title = {Construction of polylactic acid plastisphere microbiota for enhancing nitrate reduction in denitrification biofilters.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131853},
doi = {10.1016/j.biortech.2024.131853},
pmid = {39577778},
issn = {1873-2976},
abstract = {Developing methods for reusing biodegradable plastics, like polylactic acid (PLA) straws, is highly needed. Here, PLAs were applied to substitute traditional commercial ceramic media (CCM) in denitrification biofilters. During long-term operation, replacing CCM with PLA significantly enhanced nitrate removal efficiency from 32.68-54.39 % to 41.64-66.26 %. Ammonia nitrogen effluent maintained below 0.5 mg/L in all reactors. PLA plastisphere shaped unique microbial communities, i.e., denitrifying bacteria Bacillus, Pseudomonas and Acidovorax preferred to inhabit or degrade PLA. Compared to CCM biofilms, PLA diminished the importance of stochastic process in biofilm assembly of PLA plastisphere. Metagenomic sequencing suggested that PLA biofilms possessed greater metabolic capabilities of denitrification and glycolysis compared to CCM. Additionally, Bacillus strain P01 isolated from PLA plastisphere demonstrated strong PLA depolymerization. Overall, this study revealed that PLA serves as carbon source and biofilm carrier, offering a promising approach to integrating plastic reuse with wastewater treatment.},
}
@article {pmid39577726,
year = {2024},
author = {Wang, L and Wu, Y and Zhao, ZB and Jia, T and Liu, W},
title = {Applying cross-scale regulations to Sedum plumbizincicola for strengthening the bioremediation of the agricultural soil that contaminated by electronic waste dismantling and revealing the underlying mechanisms by multi-omics.},
journal = {Environmental research},
volume = {},
number = {},
pages = {120406},
doi = {10.1016/j.envres.2024.120406},
pmid = {39577726},
issn = {1096-0953},
abstract = {Electronic waste dismantling has induced the surrounding agricultural soils suffered from combined contamination of heavy metals and organic pollutants. Lower efficiency and complex mechanisms of bioremediation remain to be resolved. Here, we adopted regulations to Sedum plumbizincicola cross aboveground and belowground scales to strengthen the bioremediation efficiency. Results showed that the S. plumbizincicola intercropping with the Astragalus sinicus L. that inoculated with Rhizobium had the highest performance in reduction of Cd, PBDEs and PCBs from soils by 0.11 mg/kg, 67.93 μg/kg and 38.91 μg/kg, respectively. Rhizosphere soil metabolomics analysis demonstrated that reductions in Cd and PBDEs significantly associated with 2-Methylhippuric acid and L-Saccharopine, which were involved in phenylalanine metabolism, biosynthesis of amino acids and lysine. Metagenomic analysis revealed that these functional pathways were mediated by Frankia, Mycobacterium, Blastococcus, etc. microbial taxa, which were also significantly altered by regulations. Moreover, regulation regimes significantly affected transcription genes of S. plumbizincicola. Functional annotation revealed that cross-scale regulations significantly improve bioremediation efficiency through microorganisms and metabolites in the rhizosphere and transcription genes of S. plumbizincicola, which were illustrated to promote plant growth and tolerance to environmental stress. Our integration of multi-omics provides comprehensive and deep insights into molecular mechanisms in the cross-scale regulations of S. plumbizincicola, which would favor remediation techniques advances for the soil contaminated by electronic waste dismantling.},
}
@article {pmid39577583,
year = {2024},
author = {Yu, K and He, B and Xiong, J and Kan, P and Sheng, H and Zhi, S and Zhu, DZ and Yao, Z},
title = {Deciphering basic and key traits of bio-pollutants in a long-term reclaimed water headwater urban stream.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {177696},
doi = {10.1016/j.scitotenv.2024.177696},
pmid = {39577583},
issn = {1879-1026},
abstract = {Reclaimed water has been recognized as a stable water resource for ecological replenishment in riverine environment. However, information about the bio-pollutants spatial and temporal distributions and the associated risk in this environment remains insufficient. Herein, the bio-pollutant profile in a long-term reclaimed water headwater urban stream, including antibiotic resistance genes (ARGs), mobile genetic elements and pathogens, were revealed by metagenomics. Notably, the temporal variation in bio-pollutant levels exceeded spatial fluctuations, possibly due to the varied rainfall intensity. Specially, multidrug resistance genes and Acinetobacter baumannii (A. baumannii) were the dominant ARGs and pathogens, respectively, exhibiting higher abundance in the dry season, especially in the downstream of the receiving point, where the bio-risk also peaked. A. baumannii and Ralstonia solanacearum were found to be the main plasmids contributors inducing the horizontal gene transfer process in this stream. Overall, A. baumannii contributed over 50 % bio-risk values in most samples, indicating that it was the "overlord" in this headwater urban stream. This study revealed characteristics of bio-pollutants in a typical long-term reclaimed water headwater urban stream, highlighting the superiority of A. baumannii in bio-pollutants, which should be a key consideration in the bio-pollutants surveillance for reclaimed waters.},
}
@article {pmid39577582,
year = {2024},
author = {Mukherjee, S and Bhattacharya, R and Sarkar, O and Islam, S and Biswas, SR and Chattopadhyay, A},
title = {Gut microbiota perturbation and subsequent oxidative stress in gut and kidney tissues of zebrafish after individual and combined exposure to inorganic arsenic and fluoride.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {177519},
doi = {10.1016/j.scitotenv.2024.177519},
pmid = {39577582},
issn = {1879-1026},
abstract = {Chronic exposure to inorganic arsenic (iAs) and fluoride (F) affect gut health and potentially damage organs. The present study investigates the interplay between gut bacteria and oxidative stress (measured by MDA level, GSH level, catalase activity, Nrf2 translocation and expression) in zebrafish exposed to F (NaF 15 ppm) and As (As2O3 50 ppb) alone or in combination. Combined exposure to As and F reduced gut bacterial alteration and imposed less oxidative stress compared to F- exposure alone. V3-V4 metagenomic sequencing revealed Pseudomonas, Aeromonas and Plesiomonas genera dominated in As or F treated groups while As+F treated group was enriched in beneficial Lactococcus and Streptococcus genera. Functional KEGG analysis demonstrated treatment-specific changes in bacterial metabolism, host organismal systems, human diseases, as well as cellular processes of microbial community were significantly affected. When Aeromonas sp. isolated from F-treated fish gut, tagged with GFP-vector and fed (~3.2 × 10[6] CFU/ml) to untreated fish, induced oxidative stress in gut and kidney. Gut bacteria were found to both increase and mitigate iAs or F-toxicity, whereas As+F treatment promoted a protective response. Correlation analysis between gut microbial community at genus level and oxidative stress parameters of gut and kidney, showed Aeromonas and Plesiomonas genera are strongly correlated with oxidative stress (r = 0.5-0.9, p˂0.05). This study identifies microbiome biomarkers of iAs and F toxicity on gut-kidney axis.},
}
@article {pmid39577388,
year = {2024},
author = {Huang, P and Chen, Y and Yu, S and Zhou, Y},
title = {Propionic acid enhances H2 production in purple phototrophic bacteria: Insights into carbon and reducing equivalent allocation.},
journal = {Water research},
volume = {269},
number = {},
pages = {122799},
doi = {10.1016/j.watres.2024.122799},
pmid = {39577388},
issn = {1879-2448},
abstract = {Biohydrogen is gaining popularity as a clean and cost-effective energy source. Among the various production methods, photo fermentation (PF) with purple phototrophic bacteria (PPB) has shown great opportunity due to its high hydrogen yield. In practice, this yield is influenced by several factors, with the carbon source, particularly simple organic acid, being a key element that has attracted considerable research interest. Short-chain volatile fatty acids (VFAs), such as acetate, propionate, and butyrate, are widely found in waste streams and dark fermentation (DF) effluent. However, most studies on these VFAs focus mainly on performance evaluation, with few exploring the underlying mechanisms, which limits their applicability in real-world scenarios. To uncover the metabolic mechanisms, this study uses metagenomics to clarify the processes of reducing power production and distribution during substrate assimilation. Meanwhile, this study presents the impact of short-chain VFAs on biohydrogen, polyhydroxyalkanoates (PHA) and glycogen production by PPB. The results show that: (1) over long-term cultivation at similar COD consumption rates of 0.06 g COD/d, PPB possessed the highest hydrogen yield when fed with propionate (0.620 L H2·g COD[-1]) compared with butyrate (0.434) and acetate (0.361); (2) with propionate as the substrate, PPB accumulated less PHA (7 % of dry biomass) but more glycogen content (11 %), compared to butyrate (15 % PHA and 8 % glycogen) and acetate (21 % PHA and 5 % glycogen); (3) metagenomic analysis revealed that propionate resulted in the highest amounts of reducing equivalents, followed by butyrate and acetate; hydrogen production was the most efficient pathway for utilizing the reducing power with propionate, as the CO2 fixation and PHA or glycogen synthesis were ineffective for electron dissipation. This study offers insights into metabolic mechanism that could guide waste stream selection and pretreatment processes to provide favorable VFAs for the PF process, thereby enhancing PPB biohydrogen production performance in practical applications.},
}
@article {pmid39577368,
year = {2024},
author = {Yang, L and Yao, B and Zhang, S and Yang, Y and Wang, G and Pan, H and Zeng, X and Qiao, S},
title = {Division mechanism of labor in Diqing Tibetan Pigs gut microbiota for dietary fiber efficiently utilization.},
journal = {Microbiological research},
volume = {290},
number = {},
pages = {127977},
doi = {10.1016/j.micres.2024.127977},
pmid = {39577368},
issn = {1618-0623},
abstract = {The Diqing Tibetan (TP) pig is an roughage tolerance breed that inhabits an area with the highest altitude distribution in the world and can be maintained on a diet containing 90 % forage material in confined production systems. Our results showed that TP pigs had a strong capability for high-efficiency utilization of arabinose and xylose. Metagenomic analysis revealed that the secretion of carbohydrate esterases was mainly undertaken by fecal strains of Microbacterium, Alistipes, Acinetobacter, and Faecalibacterium, while Microbacterium, Prevotella, Turicibacter, Lactobacillus, Clostridium, and Streptococcus were responsible for most of the secretion of glycoside hydrolases. Then, a brand new species, which was named Microbacterium sp. Qiao 01 was captured and appeared to have the highest fiber utilization ability in vitro, degrading 36.54 % of the neutral detergent fiber in corn stover. Our results provide strong evidence that efficient utilization of dietary fiber by TP pigs is due to the emergence of highly specialized microbial strategies in the gut. Microorganisms showed preferences and a clear division of labor in the degradation process of dietary fiber. This study has great practical significance for improving the utilization efficiency of livestock feed and alleviating the tension of food insecurity.},
}
@article {pmid39577267,
year = {2024},
author = {Ngo, C and Morrell, JM and Tummaruk, P},
title = {Boar semen microbiome: Insights and potential implications.},
journal = {Animal reproduction science},
volume = {272},
number = {},
pages = {107647},
doi = {10.1016/j.anireprosci.2024.107647},
pmid = {39577267},
issn = {1873-2232},
abstract = {The pioneers of next-generation sequencing technology and bioinformatic analyses initiated a new era in microbiology research by offering profound insights into bacterial microbiome communities. In the pig farming sector, while considerable attention has been devoted to the gut microbiome and the microbiome of the female reproductive tract, research on the microbiome of boar semen remains limited. Nonetheless, published studies have provided valuable insights, serving as important references and sparking ideas for further investigations into the seminal microbiome. Factors such as breed, seasons, feed additives, hygiene management, and antibiotic use are believed to exert a notable influence on the diversity and richness of bacterial genera in the boar seminal microbiome, potentially affecting semen quality. Moreover, current shifts towards sustainability in the swine industry, coupled with global guidelines concerning the prudent use of antibiotics in stored boar semen for artificial insemination, underscore the need for insights into factors influencing seminal bacteria. The objective of this review is to elucidate the current understanding of boar bacterial contents using conventional culture methods, as well as the boar seminal microbiome through metagenomics and bioinformatics. It also aims to review specific microbiome communities, such as those in the reproductive tract and gut, and their connections to semen quality. In addition, strategic enhancements for processing boar semen doses through alternative methods to improve seminal quality are proposed.},
}
@article {pmid39577117,
year = {2024},
author = {Mommert-Tripon, M and Parraud, D and Grosbois, C and Gaymard, A and Cheynet, V and Lina, B and Oriol, G and Laurent, F and Dupré, C and Semanas, Q and Bal, A and Generenaz, L and Pons, S and Brengel-Pesce, K and Guichard, A and Mouton, W and Morfin, F and Fleurie, A and Trouillet-Assant, S},
title = {Advancing respiratory virus diagnostics: integrating the nasal IFN-I score for improved viral detection.},
journal = {EBioMedicine},
volume = {110},
number = {},
pages = {105450},
doi = {10.1016/j.ebiom.2024.105450},
pmid = {39577117},
issn = {2352-3964},
abstract = {BACKGROUND: This study aimed to demonstrate the utility of the nasal Type I interferon (IFN-I) response as a marker for respiratory viral infections (RVIs) and its potential to enhance diagnosis when combined with first-line PCR tests for Influenza A/B, RSV, and SARS-CoV-2.<br><br>METHODS: Nasopharyngeal swabs (NPS) from patients at Hospices Civils de Lyon (November 2022-April 2024) suspected of viral infections (n&#xa0;=&#xa0;788) and from healthy controls (n&#xa0;=&#xa0;53) were analysed. The IFN-I score was measured using the FILMARRAY&#xae; IFN-I pouch prototype, which detects four interferon-stimulated genes. The study evaluated the performance of the IFN-I score in detecting samples positive for viruses by first-line PCR and assessed its benefit in diagnosing RVIs in samples initially classified as negative by PCR.<br><br>FINDINGS: Out of 788 NPS included, 504 (64%) were positive with the first-line PCR tests, and IFN-I score was significantly higher in those samples (median [IQR]: 13.00 [2.76-45.40]) compared to ones collected from healthy controls (1.09 [0.67-1.30]; p&#xa0;<&#xa0;0.0001), with an area under the curve (AUC; 95% CI) of 0.92 (0.90-0.92). Moreover, out of the 284 NPS negative with first-line PCR tests, suspicion of viral infection according to IFN-I score was found in 63% of cases (178/284). Second-line test (BioFire&#xae; Respiratory Panel 2.1 plus) and viral metagenomic confirmed the presence of viruses 94% of cases.<br><br>INTERPRETATION: The study highlights the potential of integrating nasal IFN-I score into clinical workflows to improve RVI diagnosis and enhance preparedness for emerging viruses.<br><br>FUNDING: Public grant overseen by the French National Research Agency (ANR21-RHUS-08/ANR-23-CHIN-0001).},
}
@article {pmid39577061,
year = {2024},
author = {Mahanty, S and Pillay, K and Hardouin, EA and Andreou, D and Cvitanović, M and Darbha, GK and Mandal, S and Chaudhuri, P and Majumder, S},
title = {Whispers in the mangroves: Unveiling the silent impact of potential toxic metals (PTMs) on Indian Sundarbans fungi.},
journal = {Marine pollution bulletin},
volume = {209},
number = {Pt B},
pages = {117233},
doi = {10.1016/j.marpolbul.2024.117233},
pmid = {39577061},
issn = {1879-3363},
abstract = {This study investigates sediment samples from the Indian Sundarbans' mangrove habitat, where most samples were alkaline and hypersaline, except for one acidic sample. Elemental analysis revealed poor sediment quality, with elevated Enrichment Factors (2.20-9.7), Geo-accumulation indices (-2.19-1.19), Contamination Factors (0.61-3.18), and Pollution Load Indices (1.04-1.32). Toxic metal ions, including Pb, Cu, Ni, Cd, Zn, and Cr, were identified as key contributors to compromised sediment quality. These metals inhibit crucial sediment enzymes, such as CMC-cellulase, β-glucosidase, aryl sulfatase, urease, and phosphatases, essential for nutrient cycling and organic matter decomposition. A negative correlation was found between heavy metals and biodiversity, as indicated by the Shannon index, and a similar trend was observed with fungal load. The study highlights the adverse effects of persistent trace metals on the fungal community, potentially disrupting the mangrove ecosystem and suggests using manglicolous fungi as biological indicators of environmental health.},
}
@article {pmid39576476,
year = {2024},
author = {Zabolotneva, AA and Laskina, TA and Kharchev, DN and Shestopalov, AV},
title = {Effects of a Short-Term High-Fat Diet on Microbiota Biodiversity of the Small and Large Intestines of C57BL/6SPF Mice.},
journal = {Bulletin of experimental biology and medicine},
volume = {},
number = {},
pages = {},
pmid = {39576476},
issn = {1573-8221},
abstract = {Long-term high-fat diet (HFD) promotes the formation of excess body weight and disorders of lipid metabolism and causes persistent dysbiotic changes in the intestinal microbial community. Changes in eating behavior, endocrine and immune functions of the host are associated with changes in the structure and functional activity of microbial communities. Short-term HFD may also influence the composition and function of the intestinal microbiota, but data on this issue are limited, and most papers are focused on the study of the large intestinal microbiota. The present study examined the effect of short-term HFD (4 weeks) on the structure of microbial communities in the small and large intestines of 24 mice. High-throughput metagenomic sequencing was performed on 48 samples of small and large intestine contents. It was revealed that short-term HFD in mice contributed to impaired glucose tolerance and increased the diversity of microbiota in the colon, but not of the small intestine, and also led to changes in the representation of certain microbial taxa (in particular Tenericutes and Verrucomicrobia). Furthermore, short-term HFD increased blood glucose levels compared to control mice (fed a normal diet), but did not affect lipid metabolism. The results will help to assess the contribution of environmental factors to the structure of microbial communities of the small and large intestines and may also be useful for correcting dysbiotic conditions, including when prescribing therapeutic diets (for example, a ketogenic diet).},
}
@article {pmid39576436,
year = {2024},
author = {Zhou, Z and Zheng, X and Hua, Y and Guo, M and Sun, X and Huang, Y and Dong, L and Yu, S},
title = {Enhancing nitrogen removal in combined sewage overflows by using bio-fluidized bed with ceramic waste powder carriers: effects and mechanisms.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {39576436},
issn = {1614-7499},
support = {41861124004//National Natural Science Foundation of China/ ; },
abstract = {Micron-size ceramic waste powder (< 75 μm and 75-150 μm) was used as the carrier in a high-concentration powder carrier bio-fluidized bed (HPB) to treat simulated overflow sewage (CSOs). The sludge extracellular polymers (EPS), electron transfer capacity of EPS, nitrogen removal pathways, and microbiological characteristics were analyzed to gain insights into the nitrogen removal pathways and mechanisms. The results showed that only the effluent from the HPB (< 75 μm) could meet the stringent pollutant discharge standards in China of 50 mg/L for CODCr and 15 mg/L for total nitrogen from beginning to end. Meanwhile, the electrochemical performance tests indicated that the electron accepting and donating capacities of the sludge EPS in the HPB (< 75 μm) were 42.75% and 32.73% higher than those in the conventional activated sludge, meaning that ceramic powder carriers can increase the extracellular electron transfer capacity of the sludge and accelerate the denitrification process. Also, metagenomics analysis results showed that the relative abundances of the denitrification-related Nor genes were 28-39% higher in the HPB (< 75 μm) and HPB (75-150 μm) than in the conventional activated sludge (CAS). These results show that ceramic waste powders have the potential to be used as carriers in HPB systems to treat CSOs.},
}
@article {pmid39576133,
year = {2024},
author = {Kim, H and Ahn, J and Kim, J and Kang, H-S},
title = {Metagenomic insights and biosynthetic potential of Candidatus Entotheonella symbiont associated with Halichondria marine sponges.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0235524},
doi = {10.1128/spectrum.02355-24},
pmid = {39576133},
issn = {2165-0497},
abstract = {Korea, being surrounded by the sea, provides a rich habitat for marine sponges, which have been a prolific source of bioactive natural products. Although a diverse array of structurally novel natural products has been isolated from Korean marine sponges, their biosynthetic origins remain largely unknown. To explore the biosynthetic potential of Korean marine sponges, we conducted metagenomic analyses of sponges inhabiting the East Sea of Korea. This analysis revealed a symbiotic association of Candidatus Entotheonella bacteria with Halichondria sponges. Here, we report a new chemically rich Entotheonella variant, which we named Ca. Entotheonella halido. Remarkably, this symbiont makes up 69% of the microbial community in the sponge Halichondira dokdoensis. Genome-resolved metagenomics enabled us to obtain a high-quality Ca. E. halido genome, which represents the largest (12 Mb) and highest quality among previously reported Entotheonella genomes. We also identified the biosynthetic gene cluster (BGC) of the known sponge-derived Halicylindramides from the Ca. E. halido genome, enabling us to determine their biosynthetic origin. This new symbiotic association expands the host diversity and biosynthetic potential of metabolically talented bacterial genus Ca. Entotheonella symbionts.IMPORTANCEOur study reports the discovery of a new bacterial symbiont Ca. Entotheonella halido associated with the Korean marine sponge Halichondria dokdoensis. Using genome-resolved metagenomics, we recovered a high-quality Ca. E. halido MAG (Metagenome-Assembled Genome), which represents the largest and most complete Ca. Entotheonella MAG reported to date. Pangenome and BGC network analyses revealed a remarkably high BGC diversity within the Ca. Entotheonella pangenome, with almost no overlapping BGCs between different MAGs. The cryptic and genetically unique BGCs present in the Ca. Entotheonella pangenome represents a promising source of new bioactive natural products.},
}
@article {pmid39574841,
year = {2024},
author = {Chen, AS and Kim, H and Nzabarushimana, E and Shen, J and Williams, K and Gurung, J and McGoldrick, J and Burke, KE and Nguyen, LH and Staller, K and Chung, DC and Xavier, RJ and Khalili, H},
title = {Composition and Function of the Gut Microbiome in Microscopic Colitis.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.28.24316293},
pmid = {39574841},
abstract = {BACKGROUND: Microscopic colitis (MC) is a common cause of chronic diarrhea, predominantly among older adults. Emerging evidence suggests that perturbations of gut microbiome and metabolome may play an important role in MC pathogenesis.<br><br>OBJECTIVE: To comprehensively characterize alterations of the gut microbial and metabolic composition in MC.<br><br>DESIGN: We established a longitudinal cohort of adult patients with MC and two control groups of individuals - chronic diarrhea controls and age- and sex-matched controls without diarrhea. Using stool samples, gut microbiome was analyzed by whole-genome shotgun metagenomic sequencing, and gut metabolome was profiled by ultra-high performance liquid chromatography-mass spectrometry. Per-feature enrichment analyses of microbial species, metabolic pathways, and metabolites were done using multivariable linear models both cross-sectionally comparing MC to controls and longitudinally according to disease activity. Lastly, we performed multi-omics association analyses to assess the relationship between microbiome and metabolome data.<br><br>RESULTS: We included 683 participants, 131 with active MC (66 with both active and remission samples), 159 with chronic diarrhea, and 393 age- and sex-matched controls without diarrhea. The stool microbiome in active MC was characterized by a lower alpha diversity as compared to controls and the remission phase of MC. Compared to controls, we identified eight enriched species in MC, most of which were pro-inflammatory oral-typical species, such as Veillonella dispar and Haemophilus parainfluenzae . In contrast, 11 species, including anti-inflammatory microbes such as Blautia glucerasea and Bacteroides stercoris, were depleted in MC. Similarly, pro-inflammatory metabolites, including lactosylceramides, ceramides, lysophospholipids, and lysoplasmalogens were enriched in active MC as compared to controls or MC cases in remission. Multi-omics association analyses revealed strong and concordant links between microbes, their metabolic pathways, and metabolomic profiles, supporting the tight interplay between disturbances in stool microbiome and metabolome in MC.<br><br>CONCLUSION: We observed a significant shift in stool microbial and metabolomic composition in MC. Our findings could be used in the future for development of non-invasive biomarkers for diagnosing and monitoring MC and developing novel therapeutics.<br><br>Microbiome dysbiosis has been proposed to contribute to microscopic colitis (MC) pathogenesis.However, previous studies have been limited by small sample sizes, reliance on 16S rRNA sequencing technique, potential confounding by stool consistency, and lack of functional analyses of microbiome and longitudinal data. Moreover, the metabolomic composition of MC remain largely unknown.<br><br>WHAT THIS STUDY ADDS: In this largest longitudinal MC cohort with two control groups - chronic diarrhea controls and controls without diarrhea, gut microbiome of MC is characterized by a lower alpha diversity, enriched pro-inflammatory oral-typical species and depleted anti-inflammatory beneficial species.Gut metabolome of MC shows significant enrichment of pro-inflammatory metabolites, including lactosylceramides, ceramides, lysophospholipids, and lysoplasmalogens. Multi-omics analyses demonstrate strong and concordant relationships between microbes, metabolic pathways, and metabolomic profiles.<br><br>Our findings could facilitate development of non-invasive biomarkers and novel therapeutics for MC.},
}
@article {pmid39574671,
year = {2024},
author = {Ndjite, GM and Jiang, A and Ravel, C and Grant, M and Jiang, X and Hall, B},
title = {Gut Microbial Utilization of the Alternative Sweetener, D-Allulose, via AlsE.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.07.622513},
pmid = {39574671},
issn = {2692-8205},
abstract = {D-allulose, a rare sugar with emerging potential as a low-calorie sweetener, has garnered attention as an alternative to other commercially available alternative sweeteners, such as sugar alcohols, which often cause severe gastrointestinal discomfort. D-allulose-6-phosphate 3-epimerase (AlsE) is a prokaryotic enzyme that converts D-allulose-6-phosphate into D-fructose-6-phopshate, enabling its use as a carbon source. However, the taxonomic breadth of AlsE across gut bacteria remains poorly understood, hindering insights into the utilization of D-allulose by microbial communities. In this study, we provide experimental evidence showing that Clostridium innocuum is capable of D-allulose metabolism via a homologous AlsE. A bioinformatics search of 85,202 bacterial genomes identified 116 bacterial species with AlsE homologs, suggesting a limited distribution of AlsE in bacteria. Additionally, Escherichia coli contains a copy of alsE , but it does not grow on D-allulose as a sole carbon source unless alsE is heterologously expressed. A metagenomic analysis revealed that 15.8% of 3,079 adult healthy human metagenomic samples that we analyzed contained alsE , suggesting a limited prevalence of the enzyme in the gut microbiome. These results suggest that the gut microbiome has limited capacity to metabolize D-allulose via alsE , supporting its use as an alternative sweetener with minimal impact on microbial composition and gastrointestinal symptoms. This finding also enables personalized nutrition, allowing diabetic individuals to assess their gut microbiota for alsE , and manage glycemic response while reducing gastrointestinal distress.},
}
@article {pmid39574606,
year = {2024},
author = {Rodrigues, PB and de Rezende Rodovalho, V and Sencio, V and Benech, N and Creskey, M and Silva Angulo, F and Delval, L and Robil, C and Gosset, P and Machelart, A and Haas, J and Descat, A and Goosens, JF and Beury, D and Maurier, F and Hot, D and Wolowczuk, I and Sokol, H and Zhang, X and Ramirez Vinolo, MA and Trottein, F},
title = {Integrative metagenomics and metabolomics reveal age-associated gut microbiota and metabolite alterations in experimental COVID-19.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.05.622058},
pmid = {39574606},
issn = {2692-8205},
abstract = {Aging is a key contributor of morbidity and mortality during acute viral pneumonia. The potential role of age-associated dysbiosis on disease outcomes is still elusive. In the current study, we used high-resolution shotgun metagenomics and targeted metabolomics to characterize SARS-CoV-2-associated changes in the gut microbiota from young (2-month-old) and aged (22-month-old) hamsters, a valuable model of COVID-19. We show that age-related dysfunctions in the gut microbiota are linked to disease severity and long-term sequelae in older hamsters. Our data also reveal age-specific changes in the composition and metabolic activity of the gut microbiota during both the acute phase (day 7 post-infection, D7) and the recovery phase (D22) of infection. Aged hamsters exhibited the most notable shifts in gut microbiota composition and plasma metabolic profiles. Through an integrative analysis of metagenomics, metabolomics, and clinical data, we identified significant associations between bacterial taxa, metabolites and disease markers in the aged group. On D7 (high viral load and lung epithelial damage) and D22 (body weight loss and fibrosis), numerous amino acids, amino acid-related molecules, and indole derivatives were found to correlate with disease markers. In particular, a persistent decrease in phenylalanine, tryptophan, glutamic acid, and indoleacetic acid in aged animals positively correlated with poor recovery of body weight and/or lung fibrosis by D22. In younger hamsters, several bacterial taxa (Eubacterium , Oscillospiraceae , Lawsonibacter) and plasma metabolites (carnosine and cis-aconitic acid) were associated with mild disease outcomes. These findings support the need for age-specific microbiome-targeting strategies to more effectively manage acute viral pneumonia and long-term disease outcomes.},
}
@article {pmid39574598,
year = {2024},
author = {Nguyen, UT and Salamzade, R and Sandstrom, S and Swaney, MH and Townsend, EC and Wu, S and Cheong, JZA and Sardina, JA and Ludwikoski, I and Rybolt, M and Wan, H and Carlson, CM and Zaronowaki, R and Andes, DR and Currie, C and Kalan, L},
title = {Large-scale investigation for antimicrobial activity reveals novel defensive species across the healthy skin microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.04.621544},
pmid = {39574598},
issn = {2692-8205},
abstract = {The human skin microbiome constitutes a dynamic barrier that can impede pathogen invasion by producing antimicrobial natural products. Gene clusters encoding for production of secondary metabolites, biosynthetic gene clusters (BGCs), that are enriched in the human skin microbiome relative to other ecological settings, position this niche as a promising source for new natural product mining. Here, we introduce a new human microbiome isolate collection, the EPithelial Isolate Collection (EPIC). It includes a large phylogenetically diverse set of human skin-derived bacterial strains from eight body sites. This skin collection, consisting of 980 strains is larger and more diverse than existing resources, includes hundreds of rare and low-abundance species, and hundreds of unique BGCs. Using a large-scale co-culture screen to assess 8,756 pairwise interactions between skin-associated bacteria and potential pathogens, we reveal broad antifungal activity by skin microbiome members. Integrating 287 whole isolate genomes and 268 metagenomes from sampling sites demonstrates that while the distribution of BGC types is stable across body sites, specific gene cluster families (GCFs), each predicted to encode for a distinct secondary metabolite, can substantially vary. Sites that are dry or rarely moist harbor the greatest potential for discovery of novel bioactive metabolites. Among our discoveries are four novel bacterial species, three of which exert significant and broad-spectrum antifungal activity. This comprehensive isolate collection advances our understanding of the skin microbiomes biosynthetic capabilities and pathogen-fighting mechanisms, opening new avenues towards antimicrobial drug discovery and microbiome engineering.},
}
@article {pmid39574575,
year = {2024},
author = {Nickols, WA and McIver, LJ and Walsh, A and Zhang, Y and Nearing, JT and Asnicar, F and Punčochář, M and Segata, N and Nguyen, LH and Hartmann, EM and Franzosa, EA and Huttenhower, C and Thompson, KN},
title = {Evaluating metagenomic analyses for undercharacterized environments: what's needed to light up the microbial dark matter?.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.08.622677},
pmid = {39574575},
issn = {2692-8205},
abstract = {Non-human-associated microbial communities play important biological roles, but they remain less understood than human-associated communities. Here, we assess the impact of key environmental sample properties on a variety of state-of-the-art metagenomic analysis methods. In simulated datasets, all methods performed similarly at high taxonomic ranks, but newer marker-based methods incorporating metagenomic assembled genomes outperformed others at lower taxonomic levels. In real environmental data, taxonomic profiles assigned to the same sample by different methods showed little agreement at lower taxonomic levels, but the methods agreed better on community diversity estimates and estimates of the relationships between environmental parameters and microbial profiles.},
}
@article {pmid39574437,
year = {2024},
author = {Li, Y and Wang, B and Wang, Y and He, W and Wu, X and Zhang, X and Teng, X and Liu, L and Yang, H},
title = {Effect of stand age on rhizosphere microbial community assembly of dominant shrubs during sandy desert vegetation restoration.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1473503},
pmid = {39574437},
issn = {1664-462X},
abstract = {The rhizosphere microbial community helps govern biogeochemical cycling and facilitates complex plant-soil feedback. Understanding the evolutionary dynamics of microbial community structure and functional genes during vegetation succession is crucial for quantifying and understanding ecosystem processes and functions in restored sandy deserts. In this study, the rhizosphere microbial community structure of 11-66-year-old dominant shrubs in a desert revegetation area was examined using shotgun metagenomic sequencing. The interactions between the microbial community structure, functional gene abundances, soil properties, and plant characteristics of different stand ages were comprehensively investigated. The abundance of unique species first increased before subsequently decreasing with stand age, with shared species accounting for only 47.33%-59.42% of the total operational taxonomic units (OTUs). Copiotrophs such as Actinobacteria and Proteobacteria were found to dominate the rhizosphere soil microbial community, with their relative abundance accounting for 75.28%-81.41% of the total OTUs. There was a gradual shift in dominant microbial functional genes being involved in cellular processes towards those involved in environmental information processing and metabolism as stand age increased. Additionally, temporal partitioning was observed in both the microbial co-occurrence network complexity and topological parameters within the rhizosphere soil. Redundancy analysis revealed that dissolved organic carbon was the primary determinant influencing shifts in microbial community structure. Understanding the evolution of microbial community structure and function contributes to identifying potential mechanisms associating the soil microbiome with dominant sand-fixing shrubs as well as understanding the rhizosphere microbiome assembly process. These results shed light on the role of the rhizosphere microbiome in biogeochemical cycling and other ecosystem functions following revegetation of temperate sandy deserts.},
}
@article {pmid39574252,
year = {2024},
author = {Crombez, L and Descamps, A and Hirmz, H and Lambert, M and Calewaert, J and Siluk, D and Markuszewski, M and Biesemans, M and Petrella, G and Cicero, D and Cesaroni, S and Stokowy, T and Gerber, GK and Tataru, C and Naumovski, P and Elewaut, D and Van De Looverbosch, C and Calders, P and Van Den Noortgate, N and De Spiegeleer, B and Wynendaele, E and De Spiegeleer, A},
title = {The Saliva and Muscle Study (SaMu): Rationale and Protocol for Associations between Salivary Microbiome and Accelerated Muscle Ageing.},
journal = {The Journal of frailty &amp; aging},
volume = {13},
number = {4},
pages = {331-340},
doi = {10.14283/jfa.2024.75},
pmid = {39574252},
issn = {2260-1341},
mesh = {Humans ; *Saliva/microbiology ; *Sarcopenia/microbiology ; Aged ; Cross-Sectional Studies ; Male ; Female ; Muscle Strength/physiology ; Aging/physiology ; Microbiota/physiology ; Muscle, Skeletal/microbiology ; Aged, 80 and over ; },
abstract = {BACKGROUND: The gut microbiome is recognized as a pivotal factor in the pathophysiology of sarcopenia-a condition marked by the accelerated loss of muscle strength, mass and function with ageing. Despite this well-known gut-muscle axis, the potential links between other microbial ecosystems and sarcopenia remain largely unexplored. The oral microbiome has been linked to various age-related health conditions such as rheumatoid arthritis and colorectal cancer. However, its potential association with sarcopenia is unknown. The Saliva and Muscle (SaMu) study seeks to address this knowledge gap.<br><br>METHODS: The SaMu study comprises three sequential phases. In phase 1, a cross-sectional analysis will be conducted on a cohort of 200 individuals aged 70 years or older to examine the relationship between salivary microbiome and sarcopenia status. Participants will be recruited in the three main places of living: general community, assisted living facilities and nursing homes. The salivary microbiome composition will be evaluated utilizing shotgun metagenomics sequencing, while sarcopenia status will be determined through muscle mass (determined by whole-body bioelectrical impedance analysis and calf circumference), muscle strength (grip strength and the 5-times-sit-to-stand test) and physical performance (usual walking speed). In addition to investigating the microbiome composition, the study aims to elucidate microbiome functions by exploring potential omic associations with sarcopenia. To achieve this, salivary proteomics, metabolomics and quorum sensing peptidomics will be performed. Covariates that will be measured include clinical variables (sociodemographic factors, health status, health-related behaviours, oral health and quality of life) as well as blood variables (immune profiling, hormones, kidney and liver function, electrolytes and haematocrit). In phase 2, an in-depth mechanistic analysis will be performed on an envisaged subcohort of 50 participants. This analysis will explore pathways in muscle tissue using histology, genomics and transcriptomics, focusing on (maximal) 25 healthy older adults and (maximal) 25 with severe sarcopenia. Phase 3 involves a two-year clinical follow-up of the initial participants from the cross-sectional analysis, along with a resampling of blood and saliva. Additionally, secondary outcomes like falls, hospitalization and mortality will be examined.<br><br>DISCUSSION: Using a salivary multi-omics approach, SaMu primarily aims to clarify the associations between the oral microbiome and sarcopenia. SaMu is expected to contribute to the discovery of predictive biomarkers of sarcopenia as well as to the identification of potential novel targets to prevent/tackle sarcopenia. This study-protocol is submitted for registration at the ISRCTN registry.},
}
@article {pmid39574009,
year = {2024},
author = {Kim, S and Thapa, I and Ali, H},
title = {A novel computational approach for the mining of signature pathways using species co-occurrence networks in gut microbiomes.},
journal = {BMC microbiology},
volume = {24},
number = {Suppl 1},
pages = {490},
pmid = {39574009},
issn = {1471-2180},
mesh = {*Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/microbiology ; Humans ; *Computational Biology/methods ; *Metagenome ; Bacteria/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; Data Mining ; },
abstract = {BACKGROUND: Advances in metagenome sequencing data continue to enable new methods for analyzing biological systems. When handling microbial profile data, metagenome sequencing has proven to be far more comprehensive than traditional methods such as 16s rRNA data, which rely on partial sequences. Microbial community profiling can be used to obtain key biological insights that pave the way for more accurate understanding of complex systems that are critical for advancing biomedical research and healthcare. However, such attempts have mostly used partial or incomplete data to accurately capture those associations.<br><br>METHODS: This study introduces a novel computational approach for the identification of co-occurring microbial communities using the abundance and functional roles of species-level microbiome data. The proposed approach is then used to identify signature pathways associated with inflammatory bowel disease (IBD). Furthermore, we developed a computational pipeline to identify microbial species co-occurrences from metagenome data at various granularity levels.<br><br>RESULTS: When comparing the IBD group to a control group, we show that certain co-occurring communities of species are enriched for potential pathways. We also show that the identified co-occurring microbial species operate as a community to facilitate pathway enrichment.<br><br>CONCLUSIONS: The obtained findings suggest that the proposed network model, along with the computational pipeline, provide a valuable analytical tool to analyze complex biological systems and extract pathway signatures that can be used to diagnose certain health conditions.},
}
@article {pmid39574001,
year = {2024},
author = {Wu, J and Li, M and Zhou, C and Rong, J and Zhang, F and Wen, Y and Qu, J and Wu, R and Miao, Y and Niu, J},
title = {Changes in amino acid concentrations and the gut microbiota composition are implicated in the mucosal healing of ulcerative colitis and can be used as noninvasive diagnostic biomarkers.},
journal = {Clinical proteomics},
volume = {21},
number = {1},
pages = {62},
pmid = {39574001},
issn = {1542-6416},
support = {82160107//National Natural Science Foundation of China/ ; 82170550//National Natural Science Foundation of China/ ; 81960108//National Natural Science Foundation of China/ ; 2023533Q03//535 Talent Project of the First Affiliated Hospital of Kunming Medical University/ ; 2023535D06//535 Talent Project of the First Affiliated Hospital of Kunming Medical University/ ; 202201AT070273//Basic Research Projects of Yunnan Province/ ; H-2019050//Yunnan Health Training Project of High-Level Talents/ ; },
abstract = {BACKGROUND: Mucosal healing is the therapeutic target for ulcerative colitis (UC). While amino acids (AAs) and the gut microbiota are known to be involved in the pathogenesis of UC, their specific roles in mucosal healing have not been fully defined.<br><br>OBJECTIVES: To longitudinally assess the changes in AA concentrations and the gut microbiota composition in the context of mucosal healing in UC patients, with the aim of identifying new biomarkers with predictive value for mucosal healing in UC patients and providing a new theoretical basis for dietary therapy.<br><br>METHODS: A total of 15 UC patients with infliximab-induced mucosal healing were enrolled. Serum and fecal AA concentrations before and after mucosal healing were determined via targeted metabolomics. A receiver operating characteristic (ROC) curve was plotted to evaluate the value of different AAs in predicting mucosal healing in UC patients. The changes in the composition of the fecal gut microbiota were analyzed via metagenomics, and bioinformatics was used to analyze the functional genes and metabolic pathways associated with different bacterial species. Spearman correlation analyses of fecal AAs with significantly different concentrations and the differentially abundant bacterial species before and after mucosal healing were performed.<br><br>RESULTS: 1. The fecal concentrations of alanine, aspartic acid, glutamic acid, glutamine, glycine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine and valine were significantly decreased after mucosal healing. The serum concentrations of alanine, cysteine and valine significantly increased, whereas that of aspartic acid significantly decreased. Glutamic acid, leucine, lysine, methionine and threonine could accurately predict mucosal healing in UC patients, and the area under the curve (AUC) was >&#x2009;0.9. After combining the 5 amino acids, the AUC reached 0.96. 2. There were significant differences in the gut microbiota composition before and after mucosal healing in UC, characterized by an increase in the abundance of beneficial microbiota (Faecalibacterium prausnitzii and Bacteroides fragilis) and a decrease in the abundance of harmful microbiota (Enterococcus faecalis). LEfSe analysis identified 57 species that could predict mucosal healing, and the AUC was 0.7846. 3. Amino acid metabolic pathways were enriched in samples after mucosal healing, was associated with the abundance of multiple species, such as Faecalibacterium prausnitzi, Bacteroides fragilis, Bacteroides vulgatus and Alistipes putredinis. 4. The fecal concentrations of several AAs were negatively correlated with the abundance of a variety of beneficial strains, such as Bacteroides fragilis, uncultured Clostridium sp., Firmicutes bacterium CAG:103, Adlercreutzia equolifaciens, Coprococcus comes and positively correlated with the abundance of several harmful strains, such as Citrobacter freundii, Enterococcus faecalis, Klebsiella aerogenes, Salmonella enterica.<br><br>CONCLUSION: Altered concentrations of amino acids and their associations with the gut microbiota are implicated in the mucosal healing of UC patients and can serve as noninvasive diagnostic biomarkers.},
}
@article {pmid39573993,
year = {2024},
author = {Li, M and Li, Y and Li, X},
title = {The carpal tunnel syndrome caused by Arthrinium phaeospermum infection: first case report and literature review.},
journal = {BMC infectious diseases},
volume = {24},
number = {1},
pages = {1328},
pmid = {39573993},
issn = {1471-2334},
support = {No.2022020506)//Ningbo Top Medical and Health Research Program/ ; No.2022020506)//Ningbo Top Medical and Health Research Program/ ; No. 2022Z146//Ningbo Key Research and Development Program/ ; No. 2022Z146//Ningbo Key Research and Development Program/ ; },
mesh = {Humans ; Male ; *Carpal Tunnel Syndrome/surgery ; Debridement ; Middle Aged ; Flavobacteriaceae/isolation &amp; purification/genetics ; Flavobacteriaceae Infections/microbiology/drug therapy/diagnosis ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: The carpal tunnel syndrome (CTS) caused by atypical infection is a therapeutic and diagnostic challenge. Atypical clinical presentations often lead to misdiagnosis and incorrect therapy.<br><br>CASE PRESENTATION: This article reports a case of deep infection leading to CTS manifestations. A male patient was admitted for numbness and pain of the left hand. Left carpal tunnel release, median nerve decompression with synovial resection were performed. Inflamed synovium and effusion were submitted for bacterial culture and metagenomic next-generation sequencing (mNGS). The etiologic agent was identified as Arthrinium phaeospermum and the patient recovered after surgical debridement and 10 months of therapy.<br><br>CONCLUSIONS: Diagnosis of mycotic infection of the hand is challenging as the presentation is similar to other conditions. mNGS is presented as a valuable diagnostic adjunct for uncovering unusual infectious agents.},
}
@article {pmid39572861,
year = {2024},
author = {Ding, Y and Ma, RA and Zhang, R and Zhang, H and Zhang, J and Li, S and Zhang, SY},
title = {Increased antibiotic resistance gene abundance linked to intensive bacterial competition in the phyllosphere across an elevational gradient.},
journal = {Environmental microbiology reports},
volume = {16},
number = {6},
pages = {e70042},
doi = {10.1111/1758-2229.70042},
pmid = {39572861},
issn = {1758-2229},
support = {52270198//National Natural Science Foundation of China/ ; },
mesh = {*Bacteria/genetics/classification/isolation &amp; purification ; *Phylogeny ; *Microbiota/genetics ; Biodiversity ; Metagenomics ; Genes, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Ecosystem ; Altitude ; Drug Resistance, Bacterial/genetics ; },
abstract = {Antibiotic resistance genes (ARGs) are ancient and widespread in natural habitats, providing survival advantages for microbiomes under challenging conditions. In mountain ecosystems, phyllosphere bacterial communities face multiple stress conditions, and the elevational gradients of mountains represent crucial environmental gradients for studying biodiversity distribution patterns. However, the distribution patterns of ARGs in the phyllosphere along elevational gradients, and their correlation with bacterial community structures, remain poorly understood. Here, we applied metagenomic analyses to investigate the abundance and diversity of ARGs in 88 phyllosphere samples collected from Mount Tianmu, a national natural reserve. Our results showed that the abundance of ARGs in the phyllosphere increased along elevational gradients and was dominated by multidrug resistance and efflux pumps. The composition of bacterial communities, rather than plant traits or abiotic factors, significantly affected ARG abundance. Moreover, increased ARG abundance was correlated with greater phylogenetic overdispersion and a greater proportion of negative associations in the bacterial co-occurrence networks, suggesting that bacterial competition primarily shapes phyllosphere resistomes. These findings constitute a major advance in the biodiversity of phyllosphere resistomes along elevations, emphasizing the significant impact of bacterial community structure and assembly on ARG distribution, and are essential for understanding the emergence of ARGs.},
}
@article {pmid39572788,
year = {2024},
author = {Pereira, FC and Ge, X and Kristensen, JM and Kirkegaard, RH and Maritsch, K and Szamosvári, D and Imminger, S and Seki, D and Shazzad, JB and Zhu, Y and Decorte, M and Hausmann, B and Berry, D and Wasmund, K and Schintlmeister, A and Böttcher, T and Cheng, JX and Wagner, M},
title = {The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39572788},
issn = {2058-5276},
support = {10.55776; COE 7//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; ZK-57//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; Z383-B//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; 10.55776 COE 7//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; R01EB032391//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R35GM136223//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01AI141439//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; },
abstract = {Many human-targeted drugs alter the gut microbiome, leading to implications for host health. However, the mechanisms underlying these effects are not well known. Here we combined quantitative microbiome profiling, long-read metagenomics, stable isotope probing and single-cell chemical imaging to investigate the impact of two widely prescribed drugs on the gut microbiome. Physiologically relevant concentrations of entacapone, a treatment for Parkinson's disease, or loxapine succinate, used to treat schizophrenia, were incubated ex vivo with human faecal samples. Both drugs significantly impact microbial activity, more so than microbial abundance. Mechanistically, entacapone can complex and deplete available iron resulting in gut microbiome composition and function changes. Microbial growth can be rescued by replenishing levels of microbiota-accessible iron. Further, entacapone-induced iron starvation selected for iron-scavenging gut microbiome members encoding antimicrobial resistance and virulence genes. These findings reveal the impact of two under-investigated drugs on whole microbiomes and identify metal sequestration as a mechanism of drug-induced microbiome disturbance.},
}
@article {pmid39572621,
year = {2024},
author = {Rabenhorst, SHB and Ferrasi, AC and Barboza, MMO and Melo, VMM},
title = {Microbial composition of gastric lesions: differences based on Helicobacter pylori virulence profile.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {28890},
pmid = {39572621},
issn = {2045-2322},
support = {07939716/2020//Funda&#xe7;&#xe3;o Cearense de Apoio ao Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Humans ; *Helicobacter pylori/pathogenicity/genetics ; *Helicobacter Infections/microbiology/pathology ; *Stomach Neoplasms/microbiology/pathology ; *Gastritis/microbiology/pathology ; Virulence ; *Gastric Mucosa/microbiology/pathology ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Aged ; Metaplasia/microbiology ; Adult ; Gastrointestinal Microbiome ; },
abstract = {Helicobacter pylori infection is a major risk factor for gastric adenocarcinomas. In the case of the intestinal subtype, chronic gastritis and intestinal metaplasia are well-known sequential steps in carcinogenesis. H. pylori has high genetic diversity that can modulate virulence and pathogenicity in the human host as a cag Pathogenicity Island (cagPAI). However, bacterial gene combinations do not always explain the clinical presentation of the disease, indicating that other factors associated with H. pylori may play a role in the development of gastric disease. In this context, we characterized the microbial composition of patients with chronic gastritis (inactive and active), intestinal metaplasia, and gastric cancer as well as their potential association with H. pylori. To this end, 16 S rRNA metagenomic analysis was performed on gastric mucosa samples from patients with different types of lesions and normal gastric tissues. Our main finding was that H. pylori virulence status can contribute to significant differences in the constitution of the gastric microbiota between the sequential steps of the carcinogenesis cascade. Differential microbiota was observed in inactive and active gastritis dependent of the H. pylori presence and status (p = 0.000575). Pseudomonades, the most abundant order in the gastritis, was associated the presence of non-virulent H. pylori in the active gastritis. Notably, there are indicator genera according to H. pylori status that are poorly associated with diseases and provide additional evidence that the microbiota, in addition to H. pylori, is relevant to gastric carcinogenesis.},
}
@article {pmid39575140,
year = {2022},
author = {Lutz, KC and Jiang, S and Neugent, ML and De Nisco, NJ and Zhan, X and Li, Q},
title = {A Survey of Statistical Methods for Microbiome Data Analysis.},
journal = {Frontiers in applied mathematics and statistics},
volume = {8},
number = {},
pages = {},
pmid = {39575140},
issn = {2297-4687},
abstract = {In the last decade, numerous statistical methods have been developed for analyzing microbiome data generated from high-throughput next-generation sequencing technology. Microbiome data are typically characterized by zero inflation, overdispersion, high dimensionality, and sample heterogeneity. Three popular areas of interest in microbiome research requiring statistical methods that can account for the characterizations of microbiome data include detecting differentially abundant taxa across phenotype groups, identifying associations between the microbiome and covariates, and constructing microbiome networks to characterize ecological associations of microbes. These three areas are referred to as differential abundance analysis, integrative analysis, and network analysis, respectively. In this review, we highlight available statistical methods for differential abundance analysis, integrative analysis, and network analysis that have greatly advanced microbiome research. In addition, we discuss each method's motivation, modeling framework, and application.},
}
@article {pmid39572618,
year = {2024},
author = {Xiang, C and Wu, X and Li, T and Tang, X and Zhang, Y and Zeng, F and Xiang, H and Chen, T and Kuang, Z and Liu, F and Yang, T and Chen, X and Chen, J and Wu, Y and Huang, X and Wang, Y and Pan, C and Wang, Y},
title = {Effect of metagenomic next-generation sequencing on clinical outcomes in adults with severe pneumonia post-cardiac surgery: a single-center retrospective study.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {28907},
pmid = {39572618},
issn = {2045-2322},
support = {Grant no.2021YFS0380//Sichuan Science and Technology Department/ ; },
mesh = {Humans ; Male ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Female ; Middle Aged ; *Cardiac Surgical Procedures/adverse effects ; *Metagenomics/methods ; Aged ; *Pneumonia/microbiology/diagnosis ; Bronchoalveolar Lavage Fluid/microbiology ; Postoperative Complications/microbiology/diagnosis ; Adult ; Intensive Care Units ; },
abstract = {Reports on the application of metagenomic next-generation sequencing (mNGS) in adult patients with severe pneumonia after cardiac surgery remain limited. This study aimed to evaluate the clinical outcomes of mNGS analysis of bronchoalveolar lavage fluid (BALF) in such patients.A retrospective cohort study was conducted on adult patients with severe pneumonia after cardiac surgery. Samples were collected from patients in the surgical intensive care unit (SICU) of Sichuan Provincial People's Hospital between January 2019 and March 2024. Upon diagnosis of severe pneumonia, bronchoalveolar lavage fluid was obtained via bronchoscopy within 24 h. The mNGS group was composed of patients tested using mNGS and conventional microbiological tests. BALF was detected only by the conventional microbiological test (CMT) method in the CMT group, which involved examining bacterial and fungal smears and cultures at least. We reviewed a total of 4,064 cardiac surgeries, and based on the inclusion criteria, a total of 113 adult patients with severe pneumonia after cardiac surgery were included in this study. The overall positive rate detected by mNGS was significantly higher than that of the culture method (98% vs. 58%, P<0.0001). After receipt of the microbiological results, the mNGS group exhibited a higher incidence of antibiotic adjustments in comparison to the CMT group (P = 0.0021). After adjusting the treatment plan based on microbial testing results, the mNGS group showed an improvement in ventilator-free days within 28 days (P = 0.0475), with a shorter duration of invasive ventilation compared to the CMT group (P = 0.0208). The detection of mNGS can significantly improve the Acute Physiology and Chronic Health Evaluation-II (APACHE II) score (P = 0.0161) and Sequential Organ Failure Assessment (SOFA) score (P = 0.0076) on the 7th day after admission to the SICU. In this study, the mNGS group showed signs of having a positive impact on the length of stay in ICU (median: 9 days, IQR: 7-10 days vs. median: 10 days, IQR: 8-13.75 days, P = 0.0538), length of stay in Hospital (median: 20 days, IQR: 17-28 days vs. median: 25 days, IQR: 18-29 days, P = 0.1558), mortality in 28 days (19% vs. 20%, P = 0.8794), in-hospital mortality (19% vs. 22%, P = 0.7123); however, statistical analysis did not confirm these differences to be significant. mNGS could serve as a valuable complement to conventional diagnostic approaches in adult patients with severe pneumonia after cardiac surgery, potentially improving diagnostic accuracy and leading to more precise and timely interventions, with significant potential to inform clinical decision-making and enhance patient outcomes.},
}
@article {pmid39572587,
year = {2024},
author = {Yang, S and Zheng, J and Mao, H and Vinitchaikul, P and Wu, D and Chai, J},
title = {Multiomics of yaks reveals significant contribution of microbiome into host metabolism.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {133},
pmid = {39572587},
issn = {2055-5008},
mesh = {Animals ; Cattle ; *Rumen/microbiology ; *Metagenomics/methods ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Gastrointestinal Microbiome ; Metabolomics/methods ; Methane/metabolism ; Animal Feed ; Metabolome ; Microbiota ; Multiomics ; },
abstract = {An intensive feeding system might improve the production cycle of yaks. However, how intensive feeding system contributes to yak growth is unclear. Here, multi-omics, including rumen metagenomics, rumen and plasma metabolomics, were performed to classify the regulatory mechanisms of intensive feeding system on yaks. Increased growth performance were observed. Rumen metagenomics revealed that Clostridium, Methanobrevibacter, Piromyces and Anaeromyces increased in the intensively fed yaks, contributing to amino acid and carbohydrate metabolism. The grazing yaks had more cellulolytic microbes. These microbiomes were correlated with the pathways of "Alanine aspartate and glutamate metabolism" and "Pyruvate metabolism". Intensive feeding increased methane degradation functions, while grazing yaks had higher methyl metabolites associated with methane production. These rumen microbiomes and their metabolites resulted in changes in plasma metabolome, finally influencing yaks' growth. Thus, an intensive feeding system altered the rumen microbiome and metabolism as well as host metabolism, resulting in improvements of yak growth.},
}
@article {pmid39571816,
year = {2024},
author = {Arros, P and Palma, D and Gálvez-Silva, M and Gaete, A and Gonzalez, H and Carrasco, G and Coche, J and Perez, I and Castro-Nallar, E and Galbán, C and Varas, MA and Campos, M and Acuña, J and Jorquera, M and Chávez, FP and Cambiazo, V and Marcoleta, AE},
title = {Life on the edge: Microbial diversity, resistome, and virulome in soils from the union glacier cold desert.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {177594},
doi = {10.1016/j.scitotenv.2024.177594},
pmid = {39571816},
issn = {1879-1026},
abstract = {The high-latitude regions of Antarctica remain among the most remote, extreme, and least explored areas on Earth. Still, microbial life has been reported in these environments, with limited information on their genetic properties and functional capabilities. Although diverse autochthonous multidrug-resistant bacteria were found in Antarctic Peninsula soils, posing whether these soils could act as a source of resistance determinants that could emerge among pathogens, we still lack information regarding the resistome of areas closer to the South Pole. Moreover, no previous studies have evaluated the pathogenic potential of microbes inhabiting Antarctic soils. In this work, we combined metagenomic and culture-dependent approaches to investigate the microbial diversity, resistome, virulome, and mobile genetic elements (MGEs) in soils from Union Glacier, a cold desert in West Antarctica. Despite the extreme conditions, several bacterial phyla were found, predominating Actinomycetota and Pseudomonadota, with limited archaeal and fungal taxa. Contrastive with Ecology Glacier soils from King George Island, the Union Glacier soil bacterial community is significantly less diverse, mainly attributed to scarce moisture. We recovered >80 species-level representative genomes (SRGs) of predominant bacteria and an ammonia-oxidating nitrogen- and carbon-fixing archaeon from a novel species of Nitrosocosmicus. Several resistance and virulence genes were found in Union Glacier soils, similar to those in other Antarctic cold desert areas but significantly distinct from those observed in maritime Antarctica and other non-cryosphere biomes. Furthermore, we characterized bacterial isolates resistant to up to 24 clinical antibiotics, mainly Pseudomonas, Arthrobacter, Plantibacter, and Flavobacterium. Moreover, some isolates produced putative virulence factors, including siderophores, pyocyanins, and exoenzymes with hemolytic, lecithinase, protease, and DNAse activity. This evidence uncovers a largely unexplored resistome and virulome hosted by deep Antarctica's soil microbial communities and the presence of bacteria with pathogenic potential, highlighting the relevance of One Health approaches for environmental surveillance in this continent.},
}
@article {pmid39571716,
year = {2024},
author = {González-Parra, JA and Barrera-Conde, M and Kossatz, E and Veza, E and de la Torre, R and Busquets-Garcia, A and Robledo, P and Pizarro, N},
title = {Microbiota and social behavior alterations in a mouse model of down syndrome: Modulation by a synbiotic treatment.},
journal = {Progress in neuro-psychopharmacology &amp; biological psychiatry},
volume = {},
number = {},
pages = {111200},
doi = {10.1016/j.pnpbp.2024.111200},
pmid = {39571716},
issn = {1878-4216},
abstract = {Sex differences in the composition and functionality of gut microbiota are an emerging field of interest in neurodevelopmental disorders, as they may help in understanding the phenotypic disparities between males and females. This study aimed to characterize sex-related specific alterations in gut microbiota composition in a mouse model of Down syndrome (Ts65Dn mice, TS mice) through the sequencing of the PCR-amplified 16S ribosomal DNA fraction. Moreover, it intended to examine whether the modulation of gut microbiota by the administration of a synbiotic (SYN) treatment would be beneficial for the behavioral alterations observed in male and female TS mice. Our results show that male, but not female, TS mice exhibit alterations in beta diversity compared to their wild-type (WT) littermates. Sex-dependent differences are also observed in the relative abundance of the classes Bacilli and Clostridia. Administering the SYN effectively counteracts hypersociability in females, and normalizes the overall abundance of Bacilli, specifically by increasing Lactobacillaceae. On the contrary, it rescues emotional recognition deficits in male TS mice and increases the relative abundance of the families Lactobacillaceae, Streptococcaceae and Atopobiaceae. In addition, a metagenome KEGG analysis of differentially enriched pathways shows relevant changes in the cofactor biosynthesis and the amino acid synthesis categories. Finally, following SYN treatment, both male and female TS mice exhibit a robust increase in propionic acid levels compared to WT littermates. These findings suggest sex-specific mechanisms that could link gut microbiota composition with behavior in TS mice, and underscore the potential of targeted gut microbiota interventions to modulate social abnormalities in neurodevelopmental disorders.},
}
@article {pmid39571670,
year = {2024},
author = {Kané, F and Collins, J and Koné, A and Keita, NY and Cisse, I and Koné, KM and Diallo, D and Konate, I and Dabitao, DK and Diarra, B and Sanogo, I and Coulibaly, T and Diallo, M and Keita, D and Tangara, CO and Diakité, M and Dao, S and Fouth-Tchos, K and Aboulhab, J and Neal, A and Saliba-Shaw, K and Lu, XJ and Briese, T and Lipkin, WI and Guindo, I and Chen, RY and Wickiser, JK and Doumbia, S},
title = {Surveillance and agnostic capture sequencing of samples from individual with rash-associated illness in Mali indicates regional transmission of measles virus from west and Central Africa.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105691},
doi = {10.1016/j.meegid.2024.105691},
pmid = {39571670},
issn = {1567-7257},
abstract = {Measles is vaccine-preventable extremely contagious disease caused by the measles virus. High vaccination coverage is needed to prevent outbreaks of disease. Although molecular surveillance of measles is critical to characterize outbreaks and track viral evolution, few whole-genome sequences of measles virus from West Africa are available despite continual outbreaks in the region. Using VirCapSeq-VERT, an enhanced and comprehensive metagenomic sequencing technique that allows for simultaneous identification of all vertebrate viruses, 23 wild-type near-complete genomes of measles virus from across Mali were obtained from samples collected between January 2012 to October 2022. Other febrile rash illnesses were also identified by VirCapSeq-VERT, demonstrating the advantage of using broad detection agnostic methods when the clinical diagnosis is unclear. Whereas one measles virus sequence was consistent with measles vaccine-associated rash illness (VARI), the remaining 38 were classified within the B3.1 genotype. Broad surveillance throughout Mali reveals regional measles virus transmission across West and Central Africa into Mali, while local clinical testing in Bamako shows stable sequence conservation within genotype B3.1 evolving from Nigerian sequences. The genomic information generated in this study is critical in addressing the lack of whole genome sequences available in West Africa and these findings show the importance of phylogenetically tracking measles outbreaks given recent increases in measles cases globally.},
}
@article {pmid39571342,
year = {2024},
author = {Calvani, R and Giampaoli, O and Marini, F and Del Chierico, F and De Rosa, M and Conta, G and Sciubba, F and Tosato, M and Picca, A and Ciciarello, F and Galluzzo, V and Gervasoni, J and Di Mario, C and Santoro, L and Tolusso, B and Spagnoli, M and Tomassini, A and Aureli, W and Toto, F and Pane, S and Putignani, L and Miccheli, A and Marzetti, E and Landi, F and , },
title = {Beetroot juice intake positively influenced gut microbiota and inflammation but failed to improve functional outcomes in adults with long COVID: A pilot randomized controlled trial.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {43},
number = {12},
pages = {344-358},
doi = {10.1016/j.clnu.2024.11.023},
pmid = {39571342},
issn = {1532-1983},
abstract = {BACKGROUND &amp; AIMS: Long-term effects of coronavirus disease 2019 (long COVID) develop in a substantial number of people following an acute COVID-19 episode. Red beetroot juice may have positive effects on multiple pathways involved in long COVID. The aim of this pilot study was to explore the impact of beetroot juice supplementation on physical function, gut microbiota, and systemic inflammation in adults with long COVID.<br><br>METHODS: A single-center, double-blind, placebo-controlled randomized trial was conducted to test the effects of 14 days of beetroot juice supplementation, rich in nitrates and betalains, on functional and biological outcomes in adults aged between 20 and 60 years with long COVID. Participants were randomized 1:1 to receive either daily oral supplementation with 200&#xa0;mL beetroot juice (&#x223c;600&#xa0;mg nitrate) or placebo (&#x223c;60&#xa0;mg nitrate) for 14 days. The primary endpoint was the change from baseline to day 14 in a fatigue resistance test. Secondary outcomes included the distance walked on the 6-min walk test, handgrip strength, and flow-mediated dilation. Secondary endpoints also included changes from baseline in circulating inflammatory mediators and metagenomic and fecal water metabolomic profiles. Partial least squares discriminant analysis (PLS-DA) models were built to evaluate the differences in biological variables associated with the interventions.<br><br>RESULTS: Thirty-one participants were randomized in the study. Twenty-five of them (median (interquartile range) age 40 (10), 14 [56&#xa0;%] women), received either beetroot juice (15) or placebo (10) and completed the study. At 14 days, fatigue resistance significantly improved from baseline (mean difference [standard error]:&#xa0;+21.8 [3.7] s; p&#xa0;<&#xa0;0.001) with no significant differences between intervention groups. A significant increase from baseline in the distance walked on the 6-min walk test was observed (mean difference [standard error]:&#xa0;+30.0 [9.4] m; p&#xa0;=&#xa0;0.03), which was not different between groups. Flow-mediated dilation did not differ between participants who received beetroot juice and those on placebo. PLS-DA models allowed correct classification of participants with 92.2&#xa0;&#xb1;&#xa0;4.4&#xa0;% accuracy. Those who ingested red beetroot juice had a greater abundance of bacteria with well-known beneficial effects, including Akkermansia, Oscillospira, Prevotella, Roseburia, Ruminococcaceae, and Turicibacter, compared with placebo. Participants allocated to beetroot juice supplementation were also characterized by significantly higher levels of fecal nicotinate, trimethylamine, and markers of beetroot juice intake (e.g., 5,6-dihydroxyindole). Finally, higher levels of interferon gamma and macrophage inflammatory protein-1&#x3b2; were found in participants who consumed beetroot juice.<br><br>CONCLUSION: Beetroot juice supplementation for two weeks did not to induce significant improvements in functional outcomes in adults with long COVID compared with placebo. Beneficial effects were observed in both gut microbiota composition (i.e., increase in probiotic species) and inflammatory mediators.<br><br>TRIAL REGISTRATION: Trial was registered under ClinicalTrials.gov. Identifier no. NCT06535165.},
}
@article {pmid39571299,
year = {2024},
author = {Talavera Andújar, B and Pereira, SL and Busi, SB and Usnich, T and Borsche, M and Ertan, S and Bauer, P and Rolfs, A and Hezzaz, S and Ghelfi, J and Brüggemann, N and Antony, P and Wilmes, P and Klein, C and Grünewald, A and Schymanski, EL},
title = {Exploring environmental modifiers of LRRK2-associated Parkinson's disease penetrance: An exposomics and metagenomics pilot study on household dust.},
journal = {Environment international},
volume = {194},
number = {},
pages = {109151},
doi = {10.1016/j.envint.2024.109151},
pmid = {39571299},
issn = {1873-6750},
abstract = {Pathogenic variants in the Leucine-rich repeat kinase 2 (LRRK2) gene are a primary monogenic cause of Parkinson's disease (PD). However, the likelihood of developing PD with inherited LRRK2 pathogenic variants differs (a phenomenon known as "reduced penetrance"), with factors including age and geographic region, highlighting a potential role for lifestyle and environmental factors in disease onset. To investigate this, household dust samples from four different groups of individuals were analyzed using metabolomics/exposomics and metagenomics approaches: PD+/LRRK2+ (PD patients with pathogenic LRRK2 variants; n = 11), PD-/LRRK2+ (individuals with pathogenic LRRK2 variants but without PD diagnosis; n = 8), iPD (PD of unknown cause; n = 11), and a matched, healthy control group (n = 11). The dust was complemented with metabolomics and lipidomics of matched serum samples, where available. A total of 1,003 chemicals and 163 metagenomic operational taxonomic units (mOTUs) were identified in the dust samples, of which ninety chemicals and ten mOTUs were statistically significant (ANOVA p-value < 0.05). Reduced levels of 2-benzothiazolesulfonic acid (BThSO3) were found in the PD-/LRRK2+ group compared to the PD+/LRRK2+ . Among the significant chemicals tentatively identified in dust, two are hazardous chemical replacements: Bisphenol S (BPS), and perfluorobutane sulfonic acid (PFBuS). Furthermore, various lipids were found altered in serum including different lysophosphatidylethanolamines (LPEs), and lysophosphatidylcholines (LPCs), some with higher levels in the PD+/LRRK2+ group compared to the control group. A cellular study on isogenic neurons generated from a PD+/LRRK2+ patient demonstrated that BPS negatively impacts mitochondrial function, which is implicated in PD pathogenesis. This pilot study demonstrates how non-target metabolomics/exposomics analysis of indoor dust samples complemented with metagenomics can prioritize relevant chemicals that may be potential modifiers of LRRK2 penetrance.},
}
@article {pmid39571000,
year = {2024},
author = {Zapién-Campos, R and Bansept, F and Traulsen, A},
title = {Stochastic models allow improved inference of microbiome interactions from time series data.},
journal = {PLoS biology},
volume = {22},
number = {11},
pages = {e3002913},
doi = {10.1371/journal.pbio.3002913},
pmid = {39571000},
issn = {1545-7885},
abstract = {How can we figure out how the different microbes interact within microbiomes? To combine theoretical models and experimental data, we often fit a deterministic model for the mean dynamics of a system to averaged data. However, in the averaging procedure a lot of information from the data is lost-and a deterministic model may be a poor representation of a stochastic reality. Here, we develop an inference method for microbiomes based on the idea that both the experiment and the model are stochastic. Starting from a stochastic model, we derive dynamical equations not only for the average, but also for higher statistical moments of the microbial abundances. We use these equations to infer distributions of the interaction parameters that best describe the biological experimental data-improving identifiability and precision. The inferred distributions allow us to make predictions but also to distinguish between fairly certain parameters and those for which the available experimental data does not give sufficient information. Compared to related approaches, we derive expressions that also work for the relative abundance of microbes, enabling us to use conventional metagenome data, and account for cases where not a single host, but only replicate hosts, can be tracked over time.},
}
@article {pmid39570026,
year = {2024},
author = {Waterworth, SC and Solomons, GM and Kalinski, J-CJ and Madonsela, LS and Parker-Nance, S and Dorrington, RA},
title = {The unique and enigmatic spirochete symbiont of latrunculid sponges.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0084524},
doi = {10.1128/msphere.00845-24},
pmid = {39570026},
issn = {2379-5042},
abstract = {Bacterial symbionts are critical members of many marine sponge holobionts. Some sponge-associated bacterial lineages, such as Poribacteria, sponge-associated unclassified lineage (SAUL), and Tethybacterales, appear to have broad-host ranges and associate with a diversity of sponge species, while others are more species-specific, having adapted to the niche environment of their host. Host-associated spirochete symbionts that are numerically dominant have been documented in several invertebrates including termites, starfish, and corals. However, dominant spirochete populations are rare in marine sponges, having thus far been observed only in Clathrina clathrus and various species within the Latrunculiidae family, where they are co-dominant alongside Tethybacterales symbionts. This study aimed to characterize these spirochetes and their potential role in the host sponge. Analysis of metagenome-assembled genomes from eight latrunculid sponges revealed that these unusual spirochetes are relatively recent symbionts and are phylogenetically distinct from other sponge-associated spirochetes. Functional comparative analysis suggests that the host sponge may have selected for these spirochetes due to their ability to produce terpenoids and/or possible structural contributions.IMPORTANCESouth African latrunculid sponges are host to co-dominant Tethybacterales and Spirochete symbionts. While the Tethybacterales are broad-host range symbionts, the spirochetes have not been reported as abundant in any other marine sponge except Clathrina clathrus. However, spirochetes are regularly the most dominant populations in marine corals and terrestrial invertebrates where they are predicted to serve as beneficial symbionts. Here, we interrogated eight metagenome-assembled genomes of the latrunculid-associated spirochetes and found that these symbionts are phylogenetically distinct from all invertebrate-associated spirochetes. The symbiosis between the spirochetes and their sponge host appears to have been established relatively recently.},
}
@article {pmid39570022,
year = {2024},
author = {Wang, W and Wang, H and Zou, X and Liu, Y and Zheng, K and Chen, X and Wang, X and Sun, S and Yang, Y and Wang, M and Shao, H and Liang, Y},
title = {A novel virus potentially evolved from the N4-like viruses represents a unique viral family: Poorviridae.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0155924},
doi = {10.1128/aem.01559-24},
pmid = {39570022},
issn = {1098-5336},
abstract = {UNLABELLED: Pseudoalteromonas are widely distributed in marine extreme habitats and exhibit diverse extracellular protease activity, which is essential for marine biogeochemical cycles. However, our understanding of viruses that infect Pseudoalteromonas remains limited. This study isolated a virus infecting Pseudoalteromonas nigrifaciens from Xiaogang in Qingdao, China. vB_PunP_Y3 comprises a linear, double-strand DNA genome with a length of 48,854 bp, encoding 52 putative open reading frames. Transmission electron microscopy demonstrates the short-tailed morphology of vB_PunP_Y3. Phylogenetic and genome-content-based analysis indicate that vB_PunP_Y3 represents a novel virus family named as Poorviridae, along with three high-quality uncultivated viral genomes. Biogeographical analyses show that Poorviridae is distributed across five viral ecological zones, and is predominantly detected in the Antarctic, Arctic, and bathypelagic zones. Comparative genomics analyses identified three of the seven hallmark proteins of N4-like viruses (DNA polymerase, major capsid protein, and virion-encapsulated RNA polymerase) from vB_PunP_Y3, combing with the protein tertiary structures of the major capsid protein, suggesting that vB_PunP_Y3 might evolve from the N4-like viruses.<br><br>IMPORTANCE: vB_PunP_Y3 is a unique strain containing three of the seven hallmark proteins of N4-like viruses, but is grouped into a novel family-level viral cluster with three uncultured viruses from metagenomics, named Poorviridae. This study enhanced the understanding about the genetic diversity, evolution, and distribution of Pseudoalteromonas viruses and provided insights into the novel evolution mechanism of marine viruses.},
}
@article {pmid39569373,
year = {2024},
author = {Talukdar, D and Sarkar, M and Ahrodia, T and Kumar, S and De, D and Nath, S and Jana, P and Verma, J and Mehta, O and Kothidar, A and Yodhaanjali, JR and Sharma, K and Bakshi, S and Singh, U and Kshetrapal, P and Wadhwa, N and Thiruvengadam, R and , and Nair, GB and Bhatnagar, S and Mukherjee, S and Das, B},
title = {Previse preterm birth in early pregnancy through vaginal microbiome signatures using metagenomics and dipstick assays.},
journal = {iScience},
volume = {27},
number = {11},
pages = {111238},
pmid = {39569373},
issn = {2589-0042},
abstract = {Annually, in India, 13% of all newborns are preterm, accounting for 23.4% of preterm birth (PTB) globally. The composition and diversity of the vaginal microbiome have a notable degree of ethnic inequality. For understanding differences in vaginal microbiome composition and functions between adverse and normal pregnancy, we have collected, processed and sequenced 600 high vaginal swab (HVS) samples across the three trimesters of pregnancy from 140 women who delivered at term and 60 women who delivered PTB, adopting a targeted metagenomics approach. The microbial signatures in HVS samples showed Lactobacillus genera to be highly abundant in term birth (TB), while in early pregnancy the abundances of Gardnerella, Atopobium, and Sneathia were found to be high in PTB. We further extended our analysis, identified specific microbial genomic signatures, and developed a dipstick assay for rapid identification of PTB-associated microbiota in HVS samples in low-resource settings.},
}
@article {pmid39568836,
year = {2024},
author = {Xie, X and Xi, X and Zhao, D and Zhao, Y and Yi, T and Chen, D and Liu, R and Qi, L and Pan, Z and Wang, H and Zhang, H and Ding, R and Du, H},
title = {Advancing pathogen and tumor copy number variation detection through simultaneous metagenomic next-generation sequencing: A comprehensive review.},
journal = {Heliyon},
volume = {10},
number = {21},
pages = {e38826},
pmid = {39568836},
issn = {2405-8440},
abstract = {In clinical practice, timely and accurate diagnosis can effectively reduce unnecessary treatment, avoid high medical costs, and prevent adverse prognoses. However, some patients with malignant tumors and those with infection often exhibit similar symptoms, which are difficult to distinguish, posing challenges in accurate clinical diagnosis. Metagenomic next-generation sequencing (mNGS) technology has been widely applied to confirm the source of infection. Recent studies have shown that for pathogen detection, mNGS technology can be used to perform chromosomal copy number variations (CNVs) analysis in two different analytical pipelines using the same wet test. mNGS technology has further demonstrated its utility in not only the determination of pathogenic microorganisms but also of CNVs, thereby facilitating early differential diagnosis for malignant tumors. In this review, we aim to analyze the diagnostic performance of mNGS technology in the simultaneous detection of pathogenic microorganisms and CNVs in current clinical practice and discuss the advantages and limitations of mNGS-CNV dual-omics detection technology. Our review highlights the need for more large-scale prospective research data on current mNGS-CNV dual-omics detection technology to provide more evidence-based results for researchers and clinicians and to promote the greater role of this technology in future clinical practice.},
}
@article {pmid39568747,
year = {2024},
author = {Liang, X and Liu, X and Huang, Z and Qiu, F and Jiang, Y and Li, C and Deng, Z and Wu, J},
title = {Case report: Metagenomic next-generation sequencing for the diagnosis of rare Nocardia aobensis infection in a patient with immune thrombocytopenia.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1425655},
pmid = {39568747},
issn = {2296-858X},
abstract = {BACKGROUND: Nocardiosis poses a diagnostic challenge due to its rarity in clinical practice, non-specific clinical symptoms and imaging features, and the limitations of traditional detection methods. Nocardia aobensis (N. aobensis) is rarely detected in clinical samples. Metagenomic next-generation sequencing (mNGS) offers significant advantages over traditional methods for rapid and accurate diagnosis of infectious diseases, especially for rare pathogens.<br><br>CASE PRESENTATION: A 52-year-old woman with a history of immune thrombocytopenia for over 2&#x2009;years was hospitalized for recurrent fever and cough lasting for 10&#x2009;days. Her initial diagnosis on admission was community-acquired pneumonia, based on chest computed tomography findings of lung inflammation lesion. Empirical treatment with moxifloxacin and trimethoprim-sulfamethoxazole (TMP-SMZ) was initiated. However, her condition failed to improve significantly even after 1&#x2009;week of treatment. Bronchoalveolar lavage fluid (BALF) subjected to mNGS revealed the presence of N. aobensis, resulting in a diagnosis of pulmonary nocardiosis caused by N. aobensis. This diagnosis was also supported by Sanger sequencing of the BALF. After adjusting the antibiotic regimen to include TMP-SMZ in combination with imipenem, the patient's condition significantly improved. She was finally discharged with instructions to continue oral treatment with TMP-SMZ and linezolid for 6&#x2009;months. The patient's first follow-up 1&#x2009;month after discharge showed good treatment outcomes but with obvious side effects of the drugs. Consequently, the antibiotic regimen was changed to doxycycline, and the patient continued to improve.<br><br>CONCLUSION: We report the first detailed case of pulmonary nocardiosis caused by N. aobensis diagnosed by mNGS. mNGS could be an effective method that facilitates early diagnosis and timely decision-making for the treatment of nocardiosis, especially in cases that involve rare pathogens.},
}
@article {pmid39568069,
year = {2024},
author = {Bano, S and Wu, Q and Yu, S and Wang, X and Zhang, X},
title = {Soil properties drive nitrous oxide accumulation patterns by shaping denitrifying bacteriomes.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {94},
pmid = {39568069},
issn = {2524-6372},
support = {31971526//National Natural Science Foundation of China/ ; 2017YFD0200102//National Key Research and Development Program of China/ ; },
abstract = {In agroecosystems, nitrous oxide (N2O) emissions are influenced by both microbiome composition and soil properties, yet the relative importance of these factors in determining differential N2O emissions remains unclear. This study investigates the impacts of these factors on N2O emissions using two primary agricultural soils from northern China: fluvo-aquic soil (FS) from the North China Plain and black soil (BS) from Northeast China, which exhibit significant differences in physicochemical properties. In non-sterilized controls (NSC), we observed distinct denitrifying bacterial phenotypes between FS and BS, with BS exhibiting significantly higher N2O emissions. Cross-inoculation experiments were conducted by introducing extracted microbiomes into sterile recipient soils of both types to disentangle the relative contributions of soil properties and microbiomes on N2O emission potential. The results showed recipient-soil-dependent gas kinetics, with significantly higher N2O/(N2O + N2) ratios in BS compared to FS, regardless of the inoculum type. Metagenomic analysis further revealed significant shifts in denitrification genes and microbial diversity of the inoculated bacteriomes influenced by the recipient soil. The higher ratios of nirS/nosZ in FS and nirK/nosZ in BS indicated that the recipient soil dictates the formation of different denitrifying guilds. Specifically, the BS environment fosters nirK-based denitrifiers like Rhodanobacter, contributing to higher N2O accumulation, while FS supports a diverse array of denitrifiers, including Pseudomonas and Stutzerimonas, associated with complete denitrification and lower N2O emissions. This study underscores the critical role of soil properties in shaping microbial community dynamics and greenhouse gas emissions. These findings highlight the importance of considering soil physicochemical properties in managing agricultural practices to mitigate N2O emissions.},
}
@article {pmid39568064,
year = {2024},
author = {Sauma-Sánchez, T and Alcorta, J and Tamayo-Leiva, J and Díez, B and Bezuidenhout, H and Cowan, DA and Ramond, JB},
title = {Functional redundancy buffers the effect of poly-extreme environmental conditions on Southern African dryland soil microbial communities.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae157},
pmid = {39568064},
issn = {1574-6941},
abstract = {Drylands' poly-extreme conditions limit edaphic microbial diversity and functionality. Furthermore, climate change exacerbates soil desiccation and salinity in most drylands. To better understand the potential effects of these changes on dryland microbial communities, we evaluated their taxonomic and functional diversities in two Southern African dryland soils with contrasting aridity and salinity. Fungal community structure was significantly influenced by aridity and salinity, while Bacteria and Archaea only by salinity. Deterministic homogeneous selection was significantly more important for bacterial and archaeal communities' assembly in hyperarid and saline soils when compared to those from arid soils. This suggests that niche partitioning drives bacterial and archaeal communities' assembly under the most extreme conditions. Conversely, stochastic dispersal limitations drove the assembly of fungal communities. Hyperarid and saline soil communities exhibited similar potential functional capacities, demonstrating a disconnect between microbial structure and function. Structure variations could be functionally compensated by different taxa with similar functions, as implied by the high levels of functional redundancy. Consequently, while environmental selective pressures shape the dryland microbial community assembly and structures, they do not influence their potential functionality. This suggest that they are functionally stable, and that they could be functional even under harsher conditions, such as those expected with climate change.},
}
@article {pmid39567665,
year = {2024},
author = {Zhang, T and Hasegawa, Y and Waldor, MK},
title = {Enteric bacterial infection stimulates remodelling of bile metabolites to promote intestinal homeostasis.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39567665},
issn = {2058-5276},
support = {MKW//Howard Hughes Medical Institute (HHMI)/ ; },
abstract = {The liver makes bile, an aqueous solution critical for fat absorption, which is secreted into the duodenum. Despite extensive studies on bile salts, other components of bile are less well characterized. Here we used global metabolomic analysis on bile from specific-pathogen-free, germ-free, Citrobacter rodentium-infected or Listeria monocytogenes-infected mice and identified a metabolome of 812 metabolites that were altered by both microbiota and enteric infection. Hepatic transcriptomics identified enteric-infection-triggered pathways that probably underlie bile remodelling. Enteric infection increased levels of four dicarboxylates in bile, including itaconate. Analysis of Acod1[-/-] mice indicated that increased itaconate also increased tuft cell abundance, altered microbiota composition and function as detected by metagenomic analysis, and modulated host defence, leading to reduced Vibrio cholerae colonization. Our data suggest that enteric-infection-associated signals are relayed between the intestine and liver and induce transcriptional programmes that shape the bile metabolome, modifying the immunomodulatory and host defence functions of bile.},
}
@article {pmid39375368,
year = {2024},
author = {Jeong, E and Abdellaoui, N and Lim, JY and Seo, JA},
title = {The presence of a significant endophytic fungus in mycobiome of rice seed compartments.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {23367},
pmid = {39375368},
issn = {2045-2322},
support = {320036-5//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry/ ; RS-2023-00230782//Rural Development Administration/ ; },
mesh = {*Seeds/anatomy &amp; histology/microbiology ; *Mycobiome/genetics ; *Oryza/anatomy &amp; histology/classification/microbiology ; *Fungi/classification/isolation &amp; purification/pathogenicity ; Basidiomycota/physiology ; Metagenome/genetics ; Crops, Agricultural/anatomy &amp; histology/microbiology ; Analysis of Variance ; Republic of Korea ; },
abstract = {Seed microbial communities have been known to have a crucial role in the life cycle of a plant. In this study, we examined the distribution of the fungal communities in three compartments (husk, brown rice, and milled rice) of the fourteen rice seed samples. Ten fungal genera distributed throughout the three compartments of the rice seeds were identified as the core mycobiome of the rice seeds, regardless of collecting regions or cultivars. Based on the diversity analysis, the distribution of the fungal community in milled rice was found to be more diversified, evenly distributed, and differently clustered from the other two compartments. Among the core mycobiome, Moesziomyces dominated almost 80% of the fungal communities in the outer compartments of rice seeds, whereas the abundances of other endophytic pathogenic fungi declined. Our results provide that antagonistic yeast Moesziomyces may be able to control the endogenous pathogenic fungal communities in rice seeds, hence maintaining the quality of rice seeds. In addition, the distribution of fungal communities differs depending on the rice seed's compartment, indicating that the compartment can affect the distribution of the seed microbial community.},
}
@article {pmid39567534,
year = {2024},
author = {Wang, Z and Li, Z and Zhang, Y and Liao, J and Guan, K and Zhai, J and Meng, P and Tang, X and Dong, T and Song, Y},
title = {Root hair developmental regulators orchestrate drought triggered microbiome changes and the interaction with beneficial Rhizobiaceae.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {10068},
pmid = {39567534},
issn = {2041-1723},
mesh = {*Plant Roots/microbiology/metabolism ; *Droughts ; *Microbiota/physiology ; *Stress, Physiological ; Rhizobium/physiology/genetics ; Arabidopsis/microbiology/genetics/metabolism ; Metagenome ; Transcriptome ; Symbiosis ; },
abstract = {Drought is one of the most serious abiotic stresses, and emerging evidence suggest plant microbiome affects plant drought tolerance. However, there is a lack of genetic evidence regarding whether and how plants orchestrate the dynamic assembly of the microbiome upon drought. By utilizing mutants with enhanced or decreased root hair densities, we find that root hair regulators also affect drought induced root microbiome changes. Rhizobiaceae is a key biomarker taxa affected by root hair related mutants. We isolated and sequenced 1479 root associated microbes, and confirmed that several Rhizobium strains presented stress-alleviating activities. Metagenome, root transcriptome and root metabolome studies further reveal the multi-omic changes upon drought stress. We knocked out an ornithine cyclodeaminase (ocd) gene in Rhizobium sp. 4F10, which significantly dampens its stress alleviating ability. Our genetic and integrated multi-omics studies confirm the involvement of host genetic effects in reshaping a stress-alleviating root microbiome during drought, and provide mechanistic insights into Rhizobiaceae mediated abiotic stress protection.},
}
@article {pmid39566691,
year = {2024},
author = {An, X and Chen, S and Fu, J and Yang, C and Xiao, Y and Zhou, Z},
title = {Metabolic coupling of aerobic methane oxidation and short-cut nitrification and denitrification for anaerobic effluent treatment in photo-sequencing batch biofilm reactor.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131845},
doi = {10.1016/j.biortech.2024.131845},
pmid = {39566691},
issn = {1873-2976},
abstract = {This study explored the use of algae to supply oxygen in situ as an alternative to mechanical aeration for anaerobic effluent treatment in a photo-sequencing batch biofilm reactor (PSBBR). By establishing alternating aerobic (dissolved oxygen (DO) > 2 mg /L)/anoxic conditions (<0.5 mg-DO/L) through a 6-h off/6-h on biogas sparging cycle and continuous illumination (1500-3000 lx), the PSBBR achieved a significant ammonia removal rate of 15-25 mg N L[-1]d[-1]. This system demonstrated robust partial nitrification and nitrite reduction activities, coupled with aerobic methane oxidation. Metagenomic analysis revealed the enrichment of key microbial groups, including Leptolyngbyaceae, Methylocystis, Nitrosomonas and Hyphomicrobium. The key functional genes of methane (mmo, mdh, gfa, frm and fdh) and nitrogen (amo, hao, narGHI, and napAB) metabolisms were identified, while notably lacking nitrite oxidation genes. In conclusion, this study provides a promising post-treatment approach for anaerobic effluent through integrating biogas utilization with efficient nitrogen removal.},
}
@article {pmid39566612,
year = {2024},
author = {Callejas, IA and Kong, Y and Osborn, K and Hung, WC and Cira, M and Cason, T and Sloane, A and Shenkiryk, A and Masikip, A and Singh, A and Jones, A and Steele, JA and Jay, JA},
title = {The influence of urbanization and water reclamation plants on fecal indicator bacteria and antibiotic resistance in the Los Angeles River watershed: A case study with complementary monitoring methods.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {177577},
doi = {10.1016/j.scitotenv.2024.177577},
pmid = {39566612},
issn = {1879-1026},
abstract = {Urban land use and water reclamation plants (WRPs) can impact fecal indicator bacteria (FIB) and antimicrobial resistance (AMR) in coastal watersheds. However, there is a lack of studies exploring these effects on the US West Coast. Additionally, there is limited research using a complementary approach across culture-, qPCR-, and metagenomics-based techniques for characterizing environmental AMR. In this study, sixteen locations were sampled in the Los Angeles River, encompassing both upstream and downstream of three WRPs discharging into the river. Culture-dependent methods quantified Enterococcus, total coliforms, E. coli, and extended spectrum beta-lactamase-producing E. coli as a low-cost screening tool for AMR, while qPCR measured selected antibiotic resistance genes (ARGs): sul1, ermF, tetW, blaSHV, along with intI1 and 16S rRNA genes. Bacteroides HF183 and crAssphage markers were quantified via ddPCR. All samples underwent shotgun sequencing to investigate gene abundance and mobility and an overall risk score for AMR. Results reveal downstream sites contain ARGs at least two orders of magnitude greater than upstream locations. Developed areas had the highest ARG sequence abundances and the most ARG classes as indicated by metagenomic analysis. WRP effluent exhibited elevated ARGs and co-location of ARGs, mobile genetic elements, and pathogens. A culture-based assessment of AR in E. coli and Pseudomonas aeruginosa revealed increased resistance ratios for most antibiotics from upstream to downstream a WRP discharge point. This study highlights the impacts of land use and WRPs on ARGs and FIB, offering a multi-pronged analysis of AMR.},
}
@article {pmid39566543,
year = {2024},
author = {Uemura, T and Kawashima, A and Jingushi, K and Motooka, D and Saito, T and Sassi, N and Horibe, Y and Yamamoto, A and Liu, Y and Tani, M and Yoshimura, A and Oka, T and Okuda, Y and Yamamichi, G and Ishizuya, Y and Yamamoto, Y and Kato, T and Hatano, K and Tsujikawa, K and Wada, H and Nonomura, N},
title = {Bacterial information in serum extracellular vesicles reflects the inflammation of adherent perinephric fat.},
journal = {Cancer science},
volume = {},
number = {},
pages = {},
doi = {10.1111/cas.16410},
pmid = {39566543},
issn = {1349-7006},
support = {JP2120988 and JP22K09469//Japan Society for the Promotion of Science/ ; },
abstract = {Adipose tissue and bacterial flora are involved in metabolism in the human body. However, the relationship between the two remains unclear. Recently, the presence of circulating bacterial DNAs has been reported. We previously reported the utility of bacterial DNA in serum extracellular vesicles (EVs) for diagnosing patients with renal cell carcinoma (RCC). In this study, we aimed to assess whether there is a correlation between bacterial DNA in serum EVs and inflammation in adipose tissue. We undertook 16S rRNA metagenomic analysis of bacterial DNA in serum EVs from 77 patients with RCC (the derivation cohort). We discovered that DNAs from Enterobacteriaceae, Polaromonas, and Coxiellaceae were highly expressed in patients with low Mayo adhesive probability (MAP) scores. A lower MAP score reflects a reduced risk of dense adipose tissue and adhesions. Additionally, we combined these bacterial DNAs to create the EPC (Enterobacteriaceae, Polaromonas, Coxiellaceae) index that predicts a MAP score of 0. Subsequently, we undertook 16S rRNA metagenomic analysis of bacterial DNA in serum EVs from 32 patients with RCC (the validation cohort). The EPC index could distinguish patients with low MAP scores from those with high MAP scores in the derivation (area under the curve [AUC], 0.76; sensitivity, 56%; specificity, 85%) and validation (AUC, 0.81; sensitivity, 100%; specificity, 62%) cohorts. These results suggest that bacterial DNA in serum EVs could reflect the inflammation of adherent perinephric fat around the kidney.},
}
@article {pmid39566459,
year = {2024},
author = {Xian, Y and Cao, L and Lu, Y and Li, Q and Su, C and He, Y and Zhou, G and Chen, S and Gao, S},
title = {Metagenomics and metaproteomics reveal the effects of sludge types and inoculation modes on N,N-dimethylformamide degradation pathways and the microbial community involved.},
journal = {Journal of hazardous materials},
volume = {481},
number = {},
pages = {136548},
doi = {10.1016/j.jhazmat.2024.136548},
pmid = {39566459},
issn = {1873-3336},
abstract = {This study demonstrated the effects of the sludge type and inoculation method on the N,N-dimethylformamide degradation pathway and associated microbial communities. The sludge type is critical for DMF metabolism, with acclimatized aerobic sludge having a significant advantage in terms of DMF metabolism performance, whereas acclimatized anaerobic sludge has a reduced DMF metabolism capacity. Metagenomic revealed increased abundances of Methanosarcina, Pelomona and Xanthobacter in the adapted anaerobic sludge, suggesting that anaerobic sludge can utilize the methyl products produced by DMF metabolism for growth. Adapted aerobic sludge had high Mycobacterium abundance, significantly boosting DMF hydrolysis. In addition, a large number of dmfA2 genes were found in aerobic sludge, more so in acclimatized sludge, indicating stronger DMF metabolism. Conversely, acclimatized anaerobic sludge showed lower abundance of dmd-tmd and mauA/B, qhpA genes, implying long-term DMF toxicity reduced anaerobic microbial activity. Metaproteomic analysis showed that Methanosarcina and Methanomethylovorans enzymes in anaerobic sludge metabolized dimethylamine and methylamine to methane, aiding DMF degradation. In the aerobic sludge, aminohydrolase proteins, which hydrolyze DMF, were significantly upregulated. These findings provide insights into DMF wastewater treatment.},
}
@article {pmid39566458,
year = {2024},
author = {Zhang, L and Jiang, L and Yan, W and Tao, H and Yao, C and An, L and Sun, Y and Hu, T and Sun, W and Qian, X and Gu, J},
title = {Exogenous additives reshape the microbiome and promote the reduction of resistome in co-composting of pig manure and mushroom residue.},
journal = {Journal of hazardous materials},
volume = {481},
number = {},
pages = {136544},
doi = {10.1016/j.jhazmat.2024.136544},
pmid = {39566458},
issn = {1873-3336},
abstract = {Comprehensive understanding of the microbiome and resistome evolution in compost is crucial for guaranteeing the safety of organic fertilizers. Current studies using different composting systems and sequencing technologies have yielded varying conclusions on the efficacy of exogenous additives (EAs) in reducing antibiotic resistance genes (ARGs) in compost. This study employed metagenomics to investigate the impact of various EAs on microbial communities, ARGs, their coexistence with mobile genetic elements (MGEs), and ARG hosts in co-composting. Our results demonstrated that EAs significantly reshaped the microbial communities and facilitated a notable reduction in total ARG abundance and diversity, primarily by decreasing core ARGs. Cooperative rather than antagonistic relationships among bacteria. The RA changes in total ARGs are mainly caused by a decrease in the prevalence of core ARGs. Furthermore, EAs showed significant efficacy in reducing clinical ARGs, including cfxA, tetX1, cfxA6, vanA, and aac (6')-Ib', with diatomite (5 %) and zeolite (5 %) being the most effective. The effect of EAs on ARGs and microbial community assembly were stochastic processes. Composting stage and EAs jointly reduced the association between ARGs and MGEs in the composting system. The reduction of ARGs attributed to a decreased abundance of potential pathogenic ARG-associated hosts and diminished associations with MGEs. In conclusion, EAs present a straightforward and effective approach for promoting ARGs reduction in compost, offering crucial insights for assessing the environmental risks associated with the release of agricultural ARGs.},
}
@article {pmid39566443,
year = {2024},
author = {Zhang, L and Wang, B and Li, K and Su, Y and Wu, D and Zhan, M and Xie, B},
title = {The dynamics and assembly patterns of airborne pathogen communities in the municipal food waste treatment system and its risk implications.},
journal = {Environment international},
volume = {194},
number = {},
pages = {109143},
doi = {10.1016/j.envint.2024.109143},
pmid = {39566443},
issn = {1873-6750},
abstract = {While municipal solid waste (MSW) provides an ideal habitat for pathogen propagation, the dynamics and assembly of airborne pathogen communities in these environments remain largely unknown. Here, we combined amplicon and metagenomics with spatiotemporal sampling to study inhalable particulate matter-carried potential pathogenic bacteria at full-scale food waste treatment plants (FWTPs), alongside comparisons to urban air in the area. The results showed that pathogenic bacteria constituted a notable portion (64.5 % ± 20.6 %, n = 75) of the total bacterial communities in FWTPs-impacted air, with species and relative abundance 2-4 times higher than that of urban air, and contributed over 50 % of pathogens to the outdoor air. Airborne pathogen community structures were highly shaped by sampling sites (i.e. treatment units), but conserved across seasons (summer vs. winter) and particle sizes (PM2.5vs. PM10). Notably, Acinetobacter johnsonii-dominated pathogens (i.e. biofilm-related species) presented high levels of aerosolization and consistently occupied the upper-representative niches in all neutral models, highlighting their persistent exposure risk. Furthermore, pathogen community assembly was strongly driven by stochastic processes (58.8 %-96.8 %), while environmental variables explained only limited variations (3.4 %-28.7 %). In particular, the relative importance of stochastic processes clearly increased along an outdoor-to-indoor gradient (84.9 %-96.5 % vs. 71.3 %-76 %), which might be related to indoor anthropogenic activities that weaken microbial network stability and environmental filtering effects. This work enhances our knowledge of the dynamic behaviors and risk of airborne pathogen communities in MSW disposal and underscores the role of FWTPs in disseminating airborne pathogens.},
}
@article {pmid39566206,
year = {2024},
author = {Lv, N and Gong, P and Sun, H and Sun, X and Liu, Z and Xie, X and Xue, Y and Song, Y and Wu, K and Wang, T and Wu, Z and Zhang, L},
title = {Agricultural ecosystems rather than fertilization strategies drives structure and composition of the ureolytic microbial functional guilds.},
journal = {Journal of environmental management},
volume = {372},
number = {},
pages = {123148},
doi = {10.1016/j.jenvman.2024.123148},
pmid = {39566206},
issn = {1095-8630},
abstract = {Ureolytic microorganisms are significant in the transformation of soil nitrogen as they secrete urease to hydrolyze urea. This study aimed to investigate the effects of different fertilization regimes on ureolytic microbial functional guilds (bacteria, fungi, and archaea) in various agricultural ecosystems. Soil samples were collected from a long-term agricultural field experiment involving paddy and dryland soils. The experiment consisted of four fertilization treatments: nitrogen fertilizer (N), nitrogen fertilizer combined with composite urease/nitrification inhibitor (NI), nitrogen fertilizer combined with straw (NS), and nitrogen fertilizer combined with manure (NO). A metagenomic sequencing technique was used to assess the composition of ureolytic microbial functional guilds using the target ureC gene, along with the evaluation of soil physicochemical properties, the abundance of ureC genes from different microbial guilds, and the urease activity. The results showed that the NI treatment significantly increased the abundance of ureC genes from different microbial guilds in the two agricultural ecosystems compared with other fertilization treatments. In dryland soil, the abundance of ureC genes was positively correlated with urease activity. The ureolytic bacterial functional guild exhibits greater dominance at all taxonomic levels compared to the ureolytic fungal and archaeal functional guilds. The alpha diversity of ureolytic microbial functional guilds was greater in dryland soil than in paddy soil. Principal coordinate analysis showed that the structure of the ureolytic microbial functional guilds could be separated into two groups based on agricultural ecosystems. Phosphorus is a key environmental factor affecting the ureolytic microbial functional guilds in two agricultural ecosystems, and the structure of the ureolytic bacteria functional guild is more susceptible to pH. The results suggest that the structure of ureolytic microbial functional guilds is primarily determined by agricultural ecosystems rather than by fertilization treatments. Additionally, fertilization treatments across different agricultural ecosystems significantly impacted the community composition of ureolytic bacteria, fungi, and archaea microorganism.},
}
@article {pmid39565134,
year = {2024},
author = {Boshevska, G and Emmerich, P and von Possel, R and Jancheska, E and Buzharova, T and Kochinski, D and Tóth, GE and Cadar, D and Osmani, D},
title = {Genomic characterization of Orthonairovirus haemorrhagiae (Crimean-Congo hemorrhagic fever virus) outbreak in North Macedonia.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0074924},
doi = {10.1128/mra.00749-24},
pmid = {39565134},
issn = {2576-098X},
abstract = {Crimean-Congo hemorrhagic fever virus (CCHFV) is a significant tick-borne virus causing severe hemorrhagic disease with high fatality rate. This report presents the genomic characterization of CCHFV strain from North Macedonia's first outbreak in over 50 years, emphasizing the importance of genomic surveillance in tracking virus evolution and spread patterns in this region.},
}
@article {pmid39565113,
year = {2024},
author = {Nowak, VV and Hou, P and Owen, JG},
title = {Microbial communities associated with marine sponges from diverse geographic locations harbor biosynthetic novelty.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0072624},
doi = {10.1128/aem.00726-24},
pmid = {39565113},
issn = {1098-5336},
abstract = {Marine sponges are a prolific source of biologically active small molecules, many of which originate from sponge-associated bacteria. Identifying the producing bacteria is a key step in developing sustainable routes for the production of these metabolites. To facilitate the required computational analyses, we developed MetaSing, a reproducible singularity-based pipeline for assembly, identification of high-quality metagenome-assembled genomes (MAGs), and analysis of biosynthetic gene clusters (BGCs) from metagenomic short-read data. We applied this pipeline to metagenomic sequencing data from 16 marine sponges collected from New Zealand, Tonga, and the Mediterranean Sea. This analysis yielded 643 MAGs representing 510 species. Of the 2,670 BGCs identified across all samples, 70.8% were linked to a MAG. Comparison of BGCs to those identified from previously sequenced bacteria revealed high biosynthetic novelty in variety of underexplored phyla, including Poribacteria, Acidobacteriota, and Dadabacteria. Alongside the observation that each sample contains unique biosynthetic potential, this holds great promise for natural product discovery and for furthering the understanding of different sponge holobionts.IMPORTANCEDiscovery of new chemical compounds such as natural products is a crucial endeavor to combat the increasing resistance to antibiotics and other drugs. This manuscript demonstrates that microbial communities associated with marine sponges investigated in this work encode the potential to produce novel chemistry. Lesser studied bacterial taxa that are often difficult to cultivate are particularly rich in potential.},
}
@article {pmid39565095,
year = {2024},
author = {Bulka, O and Mahadevan, R and Edwards, EA},
title = {Pangenomic insights into Dehalobacter evolution and acquisition of functional genes for bioremediation.},
journal = {Microbial genomics},
volume = {10},
number = {11},
pages = {},
doi = {10.1099/mgen.0.001324},
pmid = {39565095},
issn = {2057-5858},
mesh = {*Biodegradation, Environmental ; *Phylogeny ; *Genome, Bacterial ; Evolution, Molecular ; Bacterial Proteins/genetics/metabolism ; Genomics ; Gene Transfer, Horizontal ; Metagenome ; },
abstract = {Dehalobacter is a genus of organohalide-respiring bacteria that is recognized for its fastidious growth using reductive dehalogenases (RDases). In the SC05 culture, however, a Dehalobacter population also mineralizes dichloromethane (DCM) produced by chloroform dechlorination using the mec cassette, just downstream of its active RDase. A closed genome of this DCM-mineralizing lineage has previously evaded assembly. Here, we present the genomes of two novel Dehalobacter strains, each of which was assembled from the metagenome of a distinct subculture from SC05. A pangenomic analysis of the Dehalobacter genus, including RDase synteny and phylogenomics, reveals at least five species of Dehalobacter based on average nucleotide identity, RDase and core gene synteny, as well as differential functional genes. An integration hotspot is also pinpointed in the Dehalobacter genome, in which many recombinase islands have accumulated. This nested recombinase island encodes the active RDase and mec cassette in both SC05 Dehalobacter genomes, indicating the transfer of key functional genes between species of Dehalobacter. Horizontal gene transfer between these two novel Dehalobacter strains has implications for the evolutionary history within the SC05 subcultures and of the Dehalobacter genus as a whole, especially regarding adaptation to anthropogenic chemicals.},
}
@article {pmid39564541,
year = {2024},
author = {Sujith, P and Singh, JR and Jayalakshmi, S and Kandaswamy, K and Shaik, MR and Hussain, SA and Kari, ZA and Guru, A},
title = {Metagenomics approaches in the discovery and development of new bioactive compound of 8-demethoxy-10-deoxysteffimycin from mangrove sediments.},
journal = {3 Biotech},
volume = {14},
number = {12},
pages = {303},
pmid = {39564541},
issn = {2190-572X},
abstract = {A metagenomic library consisting of 15,000 clones was constructed from the mangrove sediment. An antimicrobially active clone from the metagenomic library PS49 was identified by function- based screening. This paper presents the results of the biochemical characterization and metagenomic library screening of the marine-derived antibiotic, 8-demethoxy-10-deoxysteffimycin. Plasmid libraries were constructed, and clones were produced using a metagenomic approach. Out of 15,000 clones, 81 clones were screened for antimicrobial activity, and five potential clones were selected. The activity of one clone was characterized and named as PS49. The bioactive compounds from the selected clone were checked for antimicrobial, antioxidant, and anticancer activities. The clone PS49 was tested against various pathogens including bacteria and fungi and it showed inhibitory effects against all the tested pathogens. The antimicrobially active fractions were then crystallized and subjected to spectroscopic analysis such as FTIR, NMR and LC-MS analysis. The substance from clone PS49 has finally been recognized, and the compound from clone PS49 has been identified as 8-demethoxy-10-deoxysteffimycin. The substances isolated from the PS49 clone exhibited strong anticancer activity against skin cancer-cell lines SK-MEL2. The compounds showed a reduction in cell viability with an increase in the compound concentration. The compounds obtained from clone PS49 showed an IC50 value of 85 µg/ml.},
}
@article {pmid39564489,
year = {2024},
author = {Liu, X and Zang, Y and Fan, S and Miao, X and Fu, M and Ma, X and Li, M and Zhang, X and Wang, Z and Xiao, J},
title = {Changes in the structure of the microbial community within the phycospheric microenvironment and potential biogeochemical effects induced in the demise stage of green tides caused by Ulva prolifera.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1507660},
pmid = {39564489},
issn = {1664-302X},
abstract = {Green tides caused by Ulva prolifera occur annually in the Yellow Sea of China, and the massive amount of biomass decomposing during the demise stage of this green tide has deleterious ecological effects. Although microorganisms are considered key factors influencing algal bloom demise, an understanding of the microbial-algae interactions within the phycospheric microenvironment during this process is still lacking. Here, we focused on the variations in phycospheric microbial communities during the late stage of the green tide in three typically affected areas of the Yellow Sea via metagenomic sequencing analysis. In total, 16.9 million reads obtained from 18 metagenome samples were incorporated into the assembled contigs (13.4 Gbp). The phycosphere microbial community composition and diversity changed visibly during the demise of U. prolifera. The abundances of algae-lysing bacteria, Flavobacteriaceae at the family level and Alteromonas, Maribacter, and Vibrio at the genus level increased significantly in the phycosphere. In addition, the levels of glycoside hydrolases (GHs) and polysaccharide lyases (PLs) enzymes, which decompose U. prolifera polysaccharides in the phycosphere, were greater. Therefore, the degradation of algal polysaccharides can increase the efficiency of carbon metabolism pathways in the phycospheric microenvironment. Most of the genes detected in the phycosphere, especially norC, nrfA, and nasA, were associated with nitrogen metabolism pathways and showed dynamics related to the demise of the large amount of organic matter released by a green tide. Therefore, the demise of green tide algae may affect the potential carbon and nitrogen cycles of the phycospheric microenvironment by driving changes in the structure and diversity of microbial communities. Our research provides a novel perspective to better understand the ecological impact of U. prolifera during the green tide demise stage.},
}
@article {pmid39564488,
year = {2024},
author = {Redondo-Río, &#xc1; and Mundy, CJ and Tamames, J and Pedrós-Alió, C},
title = {Specialized Bacteroidetes dominate the Arctic Ocean during marine spring blooms.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1481702},
pmid = {39564488},
issn = {1664-302X},
abstract = {A metagenomic time series from Arctic seawater was obtained from Dease Strait, to analyse the changes in bacterioplankton caused by the summer phytoplankton bloom. Bacterial clades specialized in the metabolism of polysaccharides, such as Bacteroidetes, became dominant along the bloom. These specialized taxa quickly displaced the microbial clades that dominate nutrient-poor waters during early spring, such as Archaea, Alpha-and Gammaproteobacteria. At the functional level, phyla Bacteroidetes, Planctomycetes, and Verrucomicrobia showed higher contents of polysaccharide-degradation functions. The Bacteroidetes community shifted toward species with higher polysaccharide-degrading capabilities, targeting algal polysaccharides in summer. Regarding transporters, Bacteroidetes dominated SusC-TonB transporters and had an exclusive family of glycoside-binding proteins (SusD). These proteins were used to identify polysaccharide-utilization loci that clustered transporters and polysaccharide-active enzymes, showing a higher level of specialization toward polysaccharide use. Altogether, these genomic features point to the genetic adaptations that promote the dominance of Bacteroidetes during phytoplankton blooms.},
}
@article {pmid39563733,
year = {2024},
author = {Iwata, J and Nakai, K},
title = {Editorial: Emerging talents in computational genomics.},
journal = {Frontiers in genetics},
volume = {15},
number = {},
pages = {1512594},
doi = {10.3389/fgene.2024.1512594},
pmid = {39563733},
issn = {1664-8021},
}
@article {pmid39563700,
year = {2024},
author = {Quezada-Romegialli, C and Quiroga-Carmona, M and D'Elía, G and Harrod, C and Storz, JF},
title = {Diet of Andean Leaf-Eared Mice (Phyllotis) Living at Extreme Elevations on Atacama Volcanoes: Insights From Metagenomics, DNA Metabarcoding, and Stable Isotopes.},
journal = {Ecology and evolution},
volume = {14},
number = {11},
pages = {e70591},
pmid = {39563700},
issn = {2045-7758},
abstract = {On the flanks of > 6000 m Andean volcanoes that tower over the Atacama Desert, leaf-eared mice (Phyllotis vaccarum) live at extreme elevations that surpass known vegetation limits. The diet of these mice in these barren, hyperarid environments has been the subject of much speculation. According to the arthropod fallout hypothesis, sustenance is provided by windblown insects that accumulate in snowdrifts ("aolian deposits"). Mice may also feed on saxicolous lichen or forms of cryptic vegetation that have yet to be discovered at such high elevations. We tested hypotheses about the diet of mice living at extreme elevations on Atacama volcanoes by combining metagenomic and DNA metabarcoding analyses of gut contents with stable isotope analyses of mouse tissues. Genomic analyses of contents of the gastrointestinal tract of a live-captured mouse from the summit of Volcán Llullaillaco (6739 m) revealed an opportunistic but purely herbivorous diet, including lichens. Although we found no evidence of animal DNA in gut contents of the summit mouse, stable isotope data indicate that mice from elevations at or near vegetation limits (~5100 m) include a larger fraction of animal prey in their diet than mice from lower elevations. Some plant species detected in the gut contents of the summit mouse are known to exist at lower elevations at the base of the volcano and in the surrounding Altiplano, suggesting that they may occur at higher elevations beneath the snowpack or in other cryptic microhabitats.},
}
@article {pmid39563409,
year = {2024},
author = {Li, M and Chen, K and Chen, Y and Zhang, L and Cui, Y and Xiao, F and Liu, Z and Zhang, W and Jiang, J and Zhou, Q and Yan, J and Sun, Y and Guan, F},
title = {Integrative analysis of gut microbiome and host transcriptome reveal novel molecular signatures in Hashimoto's thyroiditis.},
journal = {Journal of translational medicine},
volume = {22},
number = {1},
pages = {1045},
pmid = {39563409},
issn = {1479-5876},
support = {82071952//Natural Science Foundation of China/ ; 82171873//Natural Science Foundation of China/ ; 82370806//Natural Science Foundation of China/ ; 82030058//Natural Science Foundation of China/ ; },
mesh = {Humans ; *Hashimoto Disease/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; *Transcriptome/genetics ; Female ; Male ; Adult ; Case-Control Studies ; MicroRNAs/genetics/metabolism ; Middle Aged ; ROC Curve ; RNA, Messenger/genetics/metabolism ; Gene Expression Profiling ; },
abstract = {BACKGROUND: Hashimoto's thyroiditis (HT) is an autoimmune disorder with unclear molecular mechanisms. While current diagnosis is well-established, understanding of the gut-thyroid axis in HT remains limited. This study aimed to uncover novel molecular signatures in HT by integrating gut metagenome and host transcriptome data (miRNA/mRNA), potentially elucidating disease pathogenesis and identifying new therapeutic targets.<br><br>METHODS: We recruited 31 early HT patients and 30 healthy controls in a two-stage study (discovery and validation). Blood and fecal samples underwent RNA and metagenomic sequencing, respectively. Integrative analysis included differential expression, weighted correlation network, correlation and random forest analyses. Regression models and ROC curve analysis were used to evaluate the significance of identified molecular signatures in HT.<br><br>RESULTS: Integrative analysis revealed subtle changes in gut microbiota diversity and composition in early HT, increased abundance of Bacillota_A and Spirochaetota at the phylum level, and significant differences in 24 genera and 67 species. Ecological network analysis indicated an imbalance in the gut microbiota with reduced inhibitory interactions against pathogenic genera in HT. Functional analysis showed changes in infection- and immune-related pathways. Three characteristic species (Salaquimonas_sp002400845, Clostridium_AI_sp002297865, and Enterocloster_citroniae) were identified as most relevant to HT. Analysis of miRNA and mRNA expression profiles uncovered pathways related to immune response, inflammation, infection, metabolism, proliferation, and thyroid cancer in HT. Based on correlations with HT and interactions between them, six characteristic RNAs (hsa-miR-548aq-3p, hsa-miR-374a-5p, GADD45A, IRS2, SMAD6, WWTR1) were identified. Furthermore, our study uncovered significant gut microbiota-host transcriptome interactions in HT, revealing enrichment in metabolic, immune, and cancer-related pathways, particularly with strong associations among those 9 key molecular signatures. The validation stage confirmed improved HT classification accuracy by combining these signatures (AUC&#x2009;=&#x2009;0.95, ACC&#x2009;=&#x2009;0.85), suggesting their potential significance in understanding HT pathogenesis.<br><br>CONCLUSION: Our study reveals novel molecular signatures linking gut microbiome and host transcriptome in HT, providing new insights into the disease pathogenesis. These findings not only enhance our understanding of the gut-thyroid axis but also suggest potential new directions for therapeutic interventions in HT.},
}
@article {pmid39563023,
year = {2024},
author = {Park, HA and Sung, J and Chang, Y and Ryu, S and Yoon, KJ and Kim, HL and Kim, HN},
title = {Metagenomic Analysis Identifies Sex-Related Gut Microbial Functions and Bacterial Taxa Associated With Skeletal Muscle Mass.},
journal = {Journal of cachexia, sarcopenia and muscle},
volume = {},
number = {},
pages = {},
doi = {10.1002/jcsm.13636},
pmid = {39563023},
issn = {2190-6009},
support = {2023R1A2C2006416//National Research Foundation of Korea/ ; },
abstract = {BACKGROUND: This study aimed to explore the association between gut microbiota functional profiles and skeletal muscle mass, focusing on sex-specific differences in a population under 65 years of age.<br><br>METHODS: Stool samples from participants were analysed using metagenomic shotgun sequencing. Skeletal muscle mass and skeletal muscle mass index (SMI) were quantified (SMI [%]&#x2009;=&#x2009;total appendage muscle mass [kg]/body weight [kg]&#x2009;&#xd7;&#x2009;100) using bioelectrical impedance analysis. Participants were categorized into SMI quartiles, and associations between gut microbiota, functional profiling and SMI were assessed by sex, adjusting for age, BMI and physical activity.<br><br>RESULTS: The cohort included 1027 participants (651 men, 376 women). In men, Escherichia coli (log2 fold change 3.08, q&#x2009;=&#x2009;0.001), Ruminococcus_B gnavus (log2 fold change 2.89, q&#x2009;=&#x2009;0.014) and Enterocloster sp001517625 (log2 fold change 2.47, q&#x2009;=&#x2009;0.026) were more abundant in the lowest SMI compared to the highest SMI group. In contrast, Bifidobacterium bifidum (log2 fold change 3.13, q&#x2009;=&#x2009;0.025) showed higher levels in the second lowest SMI group in women. Microbial pathways associated with amino acid synthesis (MET-SAM-PWY: log2 fold change 0.42; METSYN-PWY: log2 fold change 0.44; SER-GLYSYN-PWY: log2 fold change 0.20; PWY-5347: log2 fold change 0.41; P4-PWY: log2 fold change 0.53), N-acetylneuraminate degradation (log2 fold change 0.43), isoprene biosynthesis (log2 fold change 0.20) and purine nucleotide degradation and salvage (PWY-6353: log2 fold change 0.42; PWY-6608: log2 fold change 0.38; PWY66-409: log2 fold change 0.52; SALVADEHYPOX-PWY: log2 fold change 0.43) were enriched in the lowest SMI in men (q&#x2009;<&#x2009;0.10). In women, the second lowest SMI group showed enrichment in energy-related pathways, including lactic acid fermentation (ANAEROFRUCAT-PWY: log2 fold change 0.19), pentose phosphate pathway (PENTOSE-P-PWY: log2 fold change 0.30) and carbohydrate degradation (PWY-5484: log2 fold change 0.31; GLYCOLYSIS: log2 fold change 0.29; PWY-6901: log2 fold change 0.27) (q&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: This study highlights sex-specific differences in gut microbiota and functional pathways associated with SMI. These findings suggest that gut microbiota may play a role in muscle health and point toward microbiota-targeted strategies for maintaining muscle mass.},
}
@article {pmid39562866,
year = {2024},
author = {Camacho-Mateu, J and Lampo, A and Ares, S and Cuesta, JA},
title = {Nonequilibrium microbial dynamics unveil a new macroecological pattern beyond Taylor's law.},
journal = {Physical review. E},
volume = {110},
number = {4-1},
pages = {044402},
doi = {10.1103/PhysRevE.110.044402},
pmid = {39562866},
issn = {2470-0053},
mesh = {*Models, Biological ; Microbiota ; },
abstract = {We introduce a comprehensive analytical benchmark, relying on Fokker-Planck formalism, to study microbial dynamics in the presence of both biotic and abiotic forces. In equilibrium, we observe a balance between the two kinds of forces, leading to no correlations between species abundances. This implies that real microbiomes, where correlations have been observed, operate out of equilibrium. Therefore, we analyze nonequilibrium dynamics, presenting an ansatz for an approximate solution that embodies the complex interplay of forces in the system. This solution is consistent with Taylor's law as a coarse-grained approximation of the relation between species abundance and variance, but implies subtler effects, predicting unobserved structure beyond Taylor's law. Motivated by this theoretical prediction, we refine the analysis of existing metagenomic data, unveiling a novel universal macroecological pattern. Finally, we speculate on the physical origin of Taylor's law: building upon an analogy with Brownian motion theory, we propose that Taylor's law emerges as a fluctuation-growth relation resulting from equipartition of environmental resources among microbial species.},
}
@article {pmid39562308,
year = {2024},
author = {Yang, Y and Xu, P and He, W and Tao, F},
title = {Metagenomic analysis reveals houseflies as indicators for monitoring environmental antibiotic resistance genes.},
journal = {Environmental microbiology reports},
volume = {16},
number = {6},
pages = {e70032},
doi = {10.1111/1758-2229.70032},
pmid = {39562308},
issn = {1758-2229},
support = {32170105//National Natural Science Foundation of China/ ; MMLKF20-03//State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University/ ; },
mesh = {*Houseflies/microbiology/genetics ; *Metagenomics ; Animals ; *Anti-Bacterial Agents/pharmacology ; *Environmental Monitoring ; Genes, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Microbiota/genetics ; Bacteria/genetics/classification/drug effects/isolation &amp; purification ; Drug Resistance, Bacterial/genetics ; },
abstract = {Given the threat to public health posed by antibiotic resistance transmission, environmental monitoring is essential for tracking antibiotic resistance genes (ARGs). Houseflies, being ubiquitous organisms capable of carrying and disseminating ARGs, serve as suitable indicators for environmental monitoring. In this study, we employ metagenomic approaches to investigate housefly body surface samples from five typical sites associated with human activities. The investigation reveals microbiome diversity among the samples, along with variations in the occurrence and mobility potential of ARGs. Metagenomic analysis indicates that the composition of ARGs on housefly body surfaces is influenced by environmental ARGs, which may be enriched on the housefly body surface. The resistance genes related to multidrug, β-lactam, bacitracin, and tetracycline were the predominant ARGs detected, with multidrug-related ARGs consistently exhibiting dominance. Furthermore, the abundance of ARGs in the different housefly body surface samples was found to correlate with the population density and mobility of the sampling site. Natural environments exhibited the lowest ARG abundance, while areas with higher population density and limited population mobility displayed higher ARG abundance. This study emphasizes the effectiveness of houseflies as monitors for environmental ARGs and underscores their potential for assessing and controlling antibiotic resistance risks in urban environments.},
}
@article {pmid39561853,
year = {2024},
author = {Oto, J and Herranz, R and Verger, P and Roca, M and Plana, E and Miralles, M and Martínez-Sarmiento, M and Vera-Donoso, CD and Medina, P},
title = {Validation of urine p-cresol glucuronide as renal cell carcinoma non-invasive biomarker.},
journal = {Journal of proteomics},
volume = {},
number = {},
pages = {105357},
doi = {10.1016/j.jprot.2024.105357},
pmid = {39561853},
issn = {1876-7737},
abstract = {Renal cell carcinoma (RCC) stands among the most lethal urological malignancies. Most RCCs are incidentally diagnosed as initial symptoms are unspecific. Novel, minimally-invasive diagnostic and prognostic methods for RCC are needed, ideally in urine. Using UPLC-Q-ToF MS untargeted metabolomic analysis in urine, we previously revealed p-cresol glucuronide as potential RCC diagnostic marker. Additionally, urine samples one-year post-nephrectomy revealed isobutyryl-l-carnitine and L-proline betaine as potential RCC prognostic markers. Our present aim was to validate these differences in an independent cohort of RCC patients and healthy controls to strengthen their value as non-invasive biomarkers. In an independent cohort of 69 RCC patients and 52 controls we validated an increase in p-cresol glucuronide in urine from patients at diagnosis compared to controls (P = 0.0043). It remained increased one-year post-nephrectomy (P = 0.0288). The value of p-cresol glucuronide for RCC diagnosis was assessed with ROC curves analysis (AUC = 0.66, 95 % Confidence Interval 0.56-0.76). The role of isobutyryl-l-carnitine and L-proline betaine as prognostic markers could not be validated and will require a larger cohort. Our findings confirm the value of p-cresol glucuronide in urine as diagnostic marker for RCC in an independent cohort. This non-invasive method holds promise for enhancing patient care by reducing the need for potentially risky diagnostic procedures. Further metaproteomics-oriented approaches towards the tyrosine oxidation pathway and microbiota metagenomics studies may promote a holistic management of RCC. SIGNIFICANCE: Current imaging techniques available to diagnose and monitor renal cell carcinoma (RCC) are harmful for the patient given the high-radiation dose, and unspecific in low-grade tumors. Thus, novel non-invasive biomarkers with diagnostic and prognostic capabilities are of utmost importance. Herein, we have validated urine p-cresol glucuronide as diagnostic marker for RCC. This novel non-invasive biomarker could improve accurate assessments of tumor behavior, while enhancing patient outcomes by reducing discomfort and detrimental side effects.},
}
@article {pmid39561782,
year = {2024},
author = {Lee, D and Ahn, K and Yun, K and Oh, Y and Park, YS and Kim, YS and Gim, JA and Mun, S and Mun, JW and Han, K and Ahn, YJ},
title = {Aerobic bacterial group as an early-stage biomarker from faecal samples of patients with colorectal cancer without distant metastasis.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-19},
doi = {10.1163/18762891-bja00051},
pmid = {39561782},
issn = {1876-2891},
abstract = {The current approaches for detecting most colorectal polyps and early neoplasms lack sufficient sensitivity and specificity, potentially hindering treatment and ultimately reducing survival rates. Here, we performed a metagenomic analysis to identify microbiome markers in stool samples from patients with early-stage colorectal cancer (CRC). We compared the composition of gut microbiota between patients with CRC and healthy individuals, specifically focusing on patients with early-stage CRC, defined as those without core mutations (KRAS, BRAF) for CRC diagnosis, stable microsatellite instability, and distant metastasis. The aim of our study is to identify potential biomarkers from gut microbiota at different cancer stages in colorectal cancer (CRC) patients through 16S rRNA amplicon sequencing, thereby proposing a novel non-invasive method for the early diagnosis of CRC. Specific microbes were detected from groups divided based on the TNM criteria, with one group classified by tumour size only (named the T group) and another group with lymph node metastasis (named the TN group). Aerobic bacteria, such as Delftia, Stenotrophomonas, Sphingobacterium, Rhodococcus, Devosia, Ensifer, and Psychrobacter were predominantly detected in patients with CRC without lymph node metastasis. The diagnostic prediction was evaluated using the CatBoost algorithm; these microbes presented high diagnostic accuracy with a receiver operating characteristics-area under curve of 0.8, which was validated using qPCR. In conclusion, this study identified specific aerobic microbial groups as non-invasive biomarkers for early diagnosis in patients with CRC without genetic or environmental factors.},
}
@article {pmid39561704,
year = {2024},
author = {Wittmers, F and Comstock, J and Poirier, C and Needham, DM and Schulz, F and Malmstrom, R and Carlson, CA and Worden, AZ},
title = {Non-photosynthetic lineages sibling to Cyanobacteria associate with eukaryotes in the open ocean.},
journal = {Current biology : CB},
volume = {34},
number = {22},
pages = {R1133-R1134},
doi = {10.1016/j.cub.2024.09.009},
pmid = {39561704},
issn = {1879-0445},
mesh = {*Phylogeny ; *Eukaryota/genetics/classification ; Oceans and Seas ; Cyanobacteria/genetics/classification ; Bacteria/genetics/classification ; Seawater/microbiology ; Metagenome ; },
abstract = {Margulisbacteria are elusive uncultivated bacteria that have illuminated evolutionary transitions in the progenitor of Cyanobacteria, the latter being a critically important phylum that underpins oxygenic photosynthesis[1][,][2]. The non-photosynthetic Margulisbacteria were discovered in a sulfidic spring[3] and later in other habitats[4][5][6]. Currently, this candidate phylum partitions into the Riflemargulisbacteria, primarily from sediments and groundwater, the Termititenax from insect gut microbiomes, and the Marinamargulisbacteria, from marine samples[4][5][6]. We found that Marinamargulisbacteria amplicons were unusually distributed in size-fractionated samples from the sunlit photic and dark twilight zones of the ocean. Further, sequencing of wild marine protists rendered genomic information for distinct marinamargulisbacterial clades co-associated with uncultivated, non-photosynthetic Stramenopila and Opisthokonta protists. Phylogenomic analyses combining these data and available metagenome-assembled genomes (MAGs) and single-amplified genomes (SAGs) from sorted bacteria revealed new Marinamargulisbacteria lineages. The lineages delineate by their environment, forming clades comprising freshwater, marine pelagic, or sediment/hypoxic taxa. The remarkable diversity of Margulisbacteria indicates success in colonizing various habitats, potentially in a conserved strategy involving eukaryotic cells.},
}
@article {pmid39561549,
year = {2024},
author = {Liang, L and Pan, W and Mu, M and Zhang, L and Yang, X and Zhang, R and Du, L and Guo, X},
title = {Effect of microplastics concentration and size on pollutants removal and antibiotic resistance genes (ARGs) generation in constructed wetlands: A metagenomics insight.},
journal = {Journal of hazardous materials},
volume = {481},
number = {},
pages = {136555},
doi = {10.1016/j.jhazmat.2024.136555},
pmid = {39561549},
issn = {1873-3336},
abstract = {The accrual of microplastics (MPs) and antibiotics poses synergistic threats to the environment. This study systemically examined the effect of environmental-level (μg/L) MPs (90-110 µm) and nanoplastics (NPs, 700 nm) on constructed wetlands (CWs) treating oxytetracycline-contaminated wastewater via metagenomics analysis. Polystyrene (PS) MPs notably hindered the removal of nitrogen, phosphorus, and oxytetracycline, particularly at high level (1000 μg/L), with removal rates of 73.34 %, 59.59 %, and 99.34 %, respectively. Among them, the removal of NH4[+]-N decreased the most in comparison to CK, at 15.26 %. Antibiotic resistance genes (ARGs) copies/16S rRNA ranged from 0.26 to 0.42 in CWs, exceeding that found in rivers by a factor of 1.5 to 2.5 times. The relative abundance of multidrug resistance genes (mdtB, acrB, mexF, mdtC, and mexT) and tetracycline resistance genes (txtA, tetG, and tetP) exhibited a pronounced increase under MPs exposure, ranging from 0.06 to 0.14 and 0.01 to 0.08 copies/16S rRNA, respectively. Redundancy and network analyses emphasized robust associations among contaminant reduction, ARG abundance, and microbial community. Partial least squares path modeling indicated MPs exerted a more profound influence on pollutant removal (coefficient = 0.8194), microbial community (coefficient = 0.3358) and ARGs dissemination (coefficient = 0.6566) compared to NPs. MPs concentrations significantly affects pollutants removal and ARGs proliferation, and MPs with larger sizes amplified ARG dissemination. This research highlights the influence of MPs on CW-mediated wastewater treatment and ARGs accumulation, offering valuable insights for developing ecological wastewater treatment strategies tailored to multi-pollutant scenarios. These insights are fundamental in developing sustainable solutions to the adverse impacts of MPs on ecosystems.},
}
@article {pmid39561546,
year = {2024},
author = {Ma, H and Khusnutdinova, AN and Lemak, S and Chernikova, TN and Golyshina, OV and Almendral, D and Ferrer, M and Golyshin, PN and Yakunin, AF},
title = {Polyesterase activity is widespread in the family IV carboxylesterases from bacteria.},
journal = {Journal of hazardous materials},
volume = {481},
number = {},
pages = {136540},
doi = {10.1016/j.jhazmat.2024.136540},
pmid = {39561546},
issn = {1873-3336},
abstract = {Enzyme-based depolymerization of plastics, including polyesters, has emerged as a promising approach for plastic waste recycling and reducing environmental plastic pollution. Currently, most of the known polyester-degrading enzymes are represented by a few natural and engineered PETases from the carboxylesterase family V. To identify novel groups of polyesterases, we selected 25 proteins from the carboxylesterase family IV, which share 22 % to 80 % sequence identity to the metagenomic thermophilic polyesterase IS12. All purified proteins were found to be active against chromogenic para-nitrophenyl esters with a preference for short acyl chains. Screening for polyesterase activity using emulsified polyesters demonstrated the presence of hydrolytic activity against bis(benzoyloxyethyl) terephthalate (3PET), polycaprolactone (PCL), and polylactic acid (PLA) in all tested proteins. Biochemical characterization of four selected polyesterases revealed high thermostability in CBA10055, whereas the mesophilic GEN0105 exhibited higher polyesterase activity. Two ancestral variants of GEN0105 showed higher thermostability and activity against PCL and PLA, but reduced activity with amorphous PET. Furthermore, six established PETases were found to be highly active against PCL and PLA. Thus, our results indicate that polyesterase activity is widespread in the family IV carboxylesterases, and that most polyesterases are promiscuous being able to degrade different polyesters.},
}
@article {pmid39561190,
year = {2024},
author = {Ward, CM and Onetto, CA and Borneman, AR},
title = {Adaptation during the shift from entomopathogen to endosymbiont is accompanied by gene loss and intensified selection.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae251},
pmid = {39561190},
issn = {1759-6653},
abstract = {Fungi have been found to be associated with many insect species, with some species transitioning to reside within insects as symbionts. However, the evolutionary pressures and genomic consequences associated with this transition are not well understood. Pathogenic fungi of the genus Ophiocordyceps have undergone multiple, independent transitions from pathogen to endosymbiont lifestyles, where they reside within the fatty tissues of infected soft-scale insects trans-generationally without killing their hosts. To gain an understanding of the genomic adaptations underlying this life history shift, long-read sequencing was utilized to assemble the genomes of both the soft scale insect Parthenolecanium corni and its Ophiocordyceps endosymbiont from a single insect. Assembly and metagenomic-based binning produced a highly contiguous genome for Part. corni and a chromosome-level assembly for the Ophiocordyceps endosymbiont. The endosymbiont genome was characterized by 524 gene loss events compared to free-living pathogenic Ophiocordyceps relatives, with predicted roles in hyphal growth, cell wall integrity, metabolism, gene regulation and toxin production. Contrasting patterns of selection were observed between the nuclear and mitochondrial genomes specific to the endosymbiont lineage. Intensified selection was most frequently observed across orthologs in the nuclear genome, whereas selection on most mitochondrial genes was found to be relaxed. Scans for positive selection were enriched within the fatty acid metabolism pathway with associate specific selection within three adjacent enzymes catalyzing the conversion of acetoacetate to acetyl-COA, suggesting that the endosymbiont lineage is under selective pressure to effectively exploit the lipid rich environment of the insect fat bodies in which it is found.},
}
@article {pmid39560390,
year = {2024},
author = {Lin, H and Wu, L and Zhang, L and Ta, QK and Liu, P and Song, J and Yang, X},
title = {Metagenome-based diversity and functional analysis of culturable microbes in sugarcane.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0198224},
doi = {10.1128/spectrum.01982-24},
pmid = {39560390},
issn = {2165-0497},
abstract = {UNLABELLED: Sugarcane is a key crop for sugar and energy production, and understanding the diversity of its associated microbes is crucial for optimizing its growth and health. However, there is a lack of thorough investigation and use of microbial resources in sugarcane. This study conducted a comprehensive analysis of culturable microbes and their functional features in different tissues and rhizosphere soil of four diverse sugarcane species using metagenomics techniques. The results revealed significant microbial diversity in sugarcane's tissues and rhizosphere soil, including several important biomarker bacterial taxa identified, which are reported to engage in several processes that support plant growth, such as nitrogen fixation, phosphate solubilization, and the production of plant hormones. The Linear discriminant analysis Effect Size (LEfSe) studies identified unique microbial communities in different parts of the same sugarcane species, particularly Burkholderia, which exhibited significant variations across the sugarcane species. Microbial analysis of carbohydrate-active enzymes (CAZymes) indicated that genes related to sucrose metabolism were mostly present in specific bacterial taxa, including Burkholderia, Pseudomonas, Paraburkholderia, and Chryseobacterium. This study improves understanding of the diversities and functions of endophytes and rhizosphere soil microbes in sugarcane. Moreover, the approaches and findings of this study provide valuable insights for microbiome research and the use of comparable technologies in other agricultural fields.<br><br>IMPORTANCE: This work utilized metagenomics techniques for conducting a comprehensive examination of culturable microbes and their functional characteristics in various tissues and rhizosphere soil of four distinct sugarcane species. This study enhances comprehension of the diversity and functions of endophytes and rhizosphere soil microbes in sugarcane. Furthermore, the methodologies and discoveries of this work offer new perspectives for microbiome investigation and the use of similar technologies in other agricultural fields.},
}
@article {pmid39559703,
year = {2024},
author = {Chen, Y and Ma, T},
title = {Hematologic cancers and infections: how to detect infections in advance and determine the type?.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1476543},
pmid = {39559703},
issn = {2235-2988},
mesh = {Humans ; *Hematologic Neoplasms/complications ; *Biomarkers/blood ; *Mycoses/diagnosis/microbiology ; Bacterial Infections/diagnosis/microbiology ; High-Throughput Nucleotide Sequencing ; Cytokines/blood/metabolism ; Procalcitonin/blood ; },
abstract = {Infection is one of the leading causes of death in patients with hematologic cancers. Hematologic cancer patients with compromised immune systems are already susceptible to infections, which come on even more rapidly and are difficult to control after they develop neutrophil deficiencies from high-dose chemotherapy. After patients have developed an infection, the determination of the type of infection becomes a priority for clinicians. In this review, we summarize the biomarkers currently used for the prediction of infections in patients with hematologic cancers; procalcitonin, CD64, cytokines, and CD14 et al. can be used to determine bacterial infections, and (1-3)-β-D-glucan and galactomannan et al. can be used as a determination of fungal infections. We have also focused on the use of metagenomic next-generation sequencing in infections in patients with hematologic cancers, which has excellent clinical value in infection prediction and can detect microorganisms that cannot be detected by conventional testing methods such as blood cultures. Of course, we also focused on infection biomarkers that are not yet used in blood cancer patients but could be used as a future research direction, e.g., human neutrophil lipocalin, serum amyloid A, and heparin-binding protein et al. Finally, clinicians need to combine multiple infection biomarkers, the patient's clinical condition, local susceptibility to the type of infection, and many other factors to make a determination of the type of infection.},
}
@article {pmid39559340,
year = {2024},
author = {Wang, H and Ni, Z and Chang, Y},
title = {Prompt Diagnosis and Treatment of Japanese Spotted Fever with an Atypical Triad of Clinical Symptoms: A Case Report.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {5073-5077},
pmid = {39559340},
issn = {1178-6973},
abstract = {Japanese spotted fever (JSF) is a neglected and potentially fatal infectious disease. Delays in diagnosis and treatment of JSF are important causes of poor prognosis. We report a case of JSF in a 75-year-old farmer who, following autumn field work in Sichuan, China, presented with an atypical triad of clinical symptoms: high fever, petechial rash, and notably no eschar. Without appropriate diagnosis and treatment, she developed septic shock and acute respiratory distress syndrome. The diagnosis of JSF was confirmed by the identification of Rickettsia japonica by metagenomic next-generation sequencing (mNGS) of the blood. After one week of treatment with doxycycline, the patient's clinical symptoms subsided without any complaints of discomfort.},
}
@article {pmid39559335,
year = {2024},
author = {de Paula, TS and Leite, DMB and Lobo-Hajdu, G and Vacelet, J and Thompson, F and Hajdu, E},
title = {The complete mitochondrial DNA of the carnivorous sponge Lycopodina hypogea is putatively complemented by microDNAs.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e18255},
pmid = {39559335},
issn = {2167-8359},
mesh = {Animals ; *Porifera/genetics ; *DNA, Mitochondrial/genetics ; *Genome, Mitochondrial/genetics ; Gene Order ; Phylogeny ; RNA, Transfer/genetics ; },
abstract = {Carnivorous sponges (Porifera, Demospongiae, Cladorhizidae), contrary to the usual filter-feeding mechanism of sponges, are specialized in catching larger prey through adhesive surfaces or hook-like spicules. The mitochondrial DNA of sponges overall present several divergences from other metazoans, and while presenting unique features among major transitions, such as in calcarean and glass sponges, poriferan mitogenomes are relatively stable within their groups. Here, we report and discuss the mitogenome of Lycopodina hypogea (Vacelet &amp; Boury-Esnault, 1996), which greatly vary from its subordinal counterparts in both structure and gene order. This mitogenome is seemingly multipartite into three chromosomes, two of them as microDNAs. The main chromosome, chrM1, is unusually large, 31,099 bp in length, has a unique gene order within Poecilosclerida, and presents two rRNA, 13 protein and 19 tRNA coding genes. Intergenic regions comprise approximately 40% of chrM1, bearing several terminal direct and inverted repeats (TDRr and TIRs) but holding no vestiges of former mitochondrial sequences, pseudogenes, or transposable elements. The nd4l and trnI(gau) genes are likely located in microDNAs thus comprising putative mitochondrial chromosomes chrM2, 291 bp, and chrM3, 140 bp, respectively. It is unclear which processes are responsible for the remarkable features of the of L. hypogea mitogenome, including a generalized gene rearrangement, long IGRs, and putative extrachromosomal genes in microDNAs.},
}
@article {pmid39558935,
year = {2024},
author = {Balestrini, VP and Pinto, OHB and Simmons, BA and Gladden, JM and Krüger, RH and Quirino, BF},
title = {Analysis of novel bacterial metagenome-assembled genomes from lignin-degrading microbial consortia.},
journal = {Current research in microbial sciences},
volume = {7},
number = {},
pages = {100302},
pmid = {39558935},
issn = {2666-5174},
abstract = {Despite recent progress, bacterial degradation of lignin is not completely understood. To address the mechanisms that bacteria from unknown taxonomic groups use to perform lignin-monomer degradation, functional analysis of bacterial metagenome-assembled genomes from soil-derived consortia enriched for microorganisms capable of degrading lignin was performed. A total of 232 metagenome-assembled genomes were recovered. After applying quality criteria of at least 70 % genome completeness and contamination less than or equal to 10 %, 39 genomes were obtained. From these, a total of 14 genomes from bacteria of unknown classification at lower taxonomic levels (i.e., only classified to the order level or higher) were chosen for further functional analysis. A global analysis of the potential ecological functions of these bacteria was performed, followed by a detailed analysis of monolignol degradation pathways. The phylum with the highest number of genomes was Proteobacteria. The genomes presented functions consistent with soil-derived bacteria, like denitrification, with different metabolic capacities related to the sulfur, chlorine, arsenic and carbon cycles, in addition to the degradation of plant cell wall components like cellulose, hemicellulose, and lignin. The Sphingomonadales_OP 08 genome showed the greatest potential to degrade cellulose and hemicellulose, although it does not appear to be able to degrade lignin. The Actinobacteria_BY 70 genome presented the highest number of enzymes and pathways related to the degradation of monolignols; furthermore, it showed the greatest potential for aromatic ring breakage by different fission pathways. The genomes of the two Actinobacteria showed the caffeic acid pathway, an important phenolic compound presenting several biological properties, such as antimicrobial and antioxidant. To our knowledge, this is the first time this pathway has been reported in this class of bacteria.},
}
@article {pmid39558431,
year = {2024},
author = {Bennett, AE and Kelsey, S and Saup, C and Wilkins, M and Malacrinò, A},
title = {Selenium alters the gene content but not the taxonomic composition of the soil microbiome.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {92},
doi = {10.1186/s40793-024-00641-x},
pmid = {39558431},
issn = {2524-6372},
support = {NA//Ohio State University Center for Applied Plant Sciences/ ; },
abstract = {BACKGROUND: Microbiomes, essential to ecosystem processes, face strong selective forces that can drive rapid evolutionary adaptation. However, our understanding of evolutionary processes within natural systems remains limited. We investigated evolution in response to naturally occurring selenium in soils of different geological parental materials on the Western Slope of Colorado. Our study focused on examining changes in gene frequencies within microbial communities in response to selenium exposure.<br><br>RESULTS: Despite expectations of taxonomic composition shifts and increased gene content changes at high-selenium sites, we found no significant alterations in microbial diversity or community composition. Surprisingly, we observed a significant increase in differentially abundant genes within high-selenium sites.<br><br>CONCLUSIONS: These findings are suggestive that selection within microbiomes primarily drives the accumulation of genes among existing microbial taxa, rather than microbial species turnover, in response to strong stressors like selenium. Our study highlights an unusual system that allows us to examine evolution in response to the same stressor annually in a non-model system, contributing to understanding microbiome evolution beyond model systems.},
}
@article {pmid39558258,
year = {2024},
author = {Wu, HH and Zhao, PP and Wang, XM and Ren, YY and Fang, SY},
title = {Hearing loss as the first symptom of pneumonia caused by Chlamydia psittaci: a case report and literature review.},
journal = {BMC infectious diseases},
volume = {24},
number = {1},
pages = {1314},
pmid = {39558258},
issn = {1471-2334},
mesh = {Humans ; Male ; Aged ; *Chlamydophila psittaci/isolation &amp; purification/genetics ; *Psittacosis/microbiology/drug therapy/diagnosis/complications ; *Anti-Bacterial Agents/therapeutic use ; Tomography, X-Ray Computed ; Hearing Loss, Sensorineural/microbiology/drug therapy ; Doxycycline/therapeutic use ; Bronchoalveolar Lavage Fluid/microbiology ; Moxifloxacin/therapeutic use ; High-Throughput Nucleotide Sequencing ; Pneumonia, Bacterial/microbiology/drug therapy/diagnosis/complications ; },
abstract = {BACKGROUND: The typical clinical symptoms of psittacosis pneumonia include fever, dry cough, and chills. Sudden sensorineural hearing loss is a relatively uncommon condition in pneumonia caused by Chlamydia psittaci. In this study, we reported a rare case of Chlamydia psittaci pneumonia presented as hearing loss.<br><br>CASE PRESENTATION: A 65-year-old man presented to our hospital with sudden hearing loss, cough with sputum, and fever for the last three days. Chest computed tomography revealed inflammation of the left lung and poor response to broad-spectrum antibiotics. The metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified the sequence of Chlamydia psittaci. Subsequently, antibiotic treatment was adjusted to doxycycline hydrochloride and moxifloxacin, resulting in significant improvement in both hearing loss and lung infection.<br><br>CONCLUSIONS: Sudden sensorineural hearing loss as an extrapulmonary feature of Chlamydia psittaci pneumonia is extremely rare. Although the exact mechanism remains unclear, this case report described a patient with sudden bilateral sensorineural hearing loss as a presenting feature of Chlamydia psittaci pneumonia, illustrating the importance of the extrapulmonary features of atypical pneumonia. The mNGS test could provide early diagnosis. Many patients had a good prognosis with prompt and effective treatment.},
}
@article {pmid39558256,
year = {2024},
author = {Liu, Y and Fang, M and Yuan, C and Yang, Y and Yu, L and Li, Y and Hu, L and Li, J},
title = {Combining interferon-γ release assays and metagenomic next-generation sequencing for diagnosis of pulmonary tuberculosis: a retrospective study.},
journal = {BMC infectious diseases},
volume = {24},
number = {1},
pages = {1316},
pmid = {39558256},
issn = {1471-2334},
support = {2208085MH264//Natural Science Foundation in Anhui Province/ ; 2021xkj138//Project Supported by Anhui Medical University/ ; 202304295107020043//Anhui Province clinical medical research transformation special project/ ; 2024AH040114//University research project in Anhui Province/ ; 2023AH010083//Anhui university scientific research project/ ; MTP2022A015//China Primary Health Care Foundation/ ; },
mesh = {Humans ; Retrospective Studies ; Male ; Female ; *Interferon-gamma Release Tests/methods ; *Tuberculosis, Pulmonary/diagnosis/microbiology/blood ; Middle Aged ; Adult ; *High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Interferon-gamma/blood ; Sensitivity and Specificity ; Aged ; ROC Curve ; Mycobacterium tuberculosis/genetics ; },
abstract = {BACKGROUND: Rapid diagnosis of pulmonary tuberculosis (PTB) is urgently needed. We aimed to improve diagnosis rates by combining tuberculosis-interferon (IFN)-γ release assays (TB-IGRA) with metagenomic next-generation sequencing (mNGS) for PTB diagnosis.<br><br>METHODS: A retrospective study of 29 PTB and 32 non-TB patients from our hospital was conducted between October 2022 and June 2023. Samples were processed for TB-IGRA and mNGS tests according to the manufacturer's protocol.<br><br>RESULTS: The levels of IFN-&#x3b3; release in PTB patients were significantly higher than those in non-TB patients (604.15&#x2009;&#xb1;&#x2009;112.18 pg/mL, and 1.04&#x2009;&#xb1;&#x2009;0.38 pg/mL, respectively; p&#x2009;<&#x2009;0.0001). Regarding presenting symptoms or signs, cough and thoracalgia were less common in PTB patients than in non-TB patients (p&#x2009;=&#x2009;0.001 and p&#x2009;=&#x2009;0.024, respectively). Total protein and albumin levels in the sera of PTB patients were significantly elevated compared to non-TB patients (p&#x2009;=&#x2009;0.039 and p&#x2009;=&#x2009;0.004, respectively). The area under the ROC curve (AUC) for TB-IGRA in PTB diagnosis was 0.939. With an optimal IFN-&#x3b3; cut-off value of 14.3 pg/mL (Youden's index 0.831), sensitivity was 86.2% and specificity was 96.9%. ROC curve analysis for mNGS and TB-IGRA combined with mNGS showed AUCs of 0.879 and 1, respectively. The AUC of TB-IGRA combined with mNGS was higher than that of TB-IGRA and mNGS alone.<br><br>CONCLUSIONS: TB-IGRA combined with mNGS may be an effective method for diagnosing tuberculosis, and can be used in the clinical diagnosis of PTB.},
}
@article {pmid39558184,
year = {2024},
author = {Sayers, EW and Cavanaugh, M and Frisse, L and Pruitt, KD and Schneider, VA and Underwood, BA and Yankie, L and Karsch-Mizrachi, I},
title = {GenBank 2025 update.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae1114},
pmid = {39558184},
issn = {1362-4962},
support = {/NH/NIH HHS/United States ; },
abstract = {GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public data repository that contains 34 trillion base pairs from over 4.7 billion nucleotide sequences for 581 000 formally described species. Daily data exchange with the European Nucleotide Archive and the DNA Data Bank of Japan ensures worldwide coverage. We summarize the content of the database in 2025 and recent updates such as accelerated processing of influenza sequences and the ability to upload feature tables to Submission Portal for messenger RNA sequences. We provide an overview of the web, application programming and command-line interfaces that allow users to access GenBank data. We also discuss the importance of creating BioProject and BioSample records during submissions, particularly for viruses and metagenomes. Finally, we summarize educational materials and recent community outreach efforts.},
}
@article {pmid39558081,
year = {2024},
author = {Yang, M and Zhao, Y and Li, L and Qi, Y and Gao, P and Guo, J and Liu, J and Chen, Z and Zhao, J and Yu, L},
title = {Functional dynamics analysis of endophytic microbial communities during Amorphophallus muelleri seed maturation.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {28432},
pmid = {39558081},
issn = {2045-2322},
support = {YJL24014//Talent Introduction Program of Kunming University/ ; 202201AT070113//Yunnan Provincial Science and Technology Dep artment/ ; 202101AO070075//Yunnan Provincial Science and Technology Dep artment/ ; 202401AU070020//Yunnan Provincial Science and Technology Dep artment/ ; 202201AU070043//Yunnan Provincial Science and Technology Dep artment/ ; 202101BA070001-174//Yunnan Provincial Science and Technology Dep artment/ ; 202301AU070136//Yunnan Provincial Science and Technology Dep artment/ ; 2022J0644//Yunnan Education Department Research Project/ ; 2023J0827//Yunnan Education Department Research Project/ ; YNWR-QNBJ-2018-324//Yunnan Province Youth Talent Support Program/ ; },
abstract = {Konjac seeds of Amorphophallus muelleri are produced through a unique form of apomixis in triploid parthenogenesis, and typically require a longer maturation period (approximately 8 months). To date, the relevant functions of endophytic microbial taxa during A. muelleri seed development and maturation remain largely unexplored. In this study, we analyzed the functional adaptability and temporal dynamics of endophytic microbial communities during three stages of A. muelleri seed maturation. Through metagenomic sequencing, we determined that the functions of the endophytic microbiome in A. muelleri seeds were driven by the seed maturation status, and the functions of the microbial communities in the seed coats and seeds differed significantly. The species annotation results show that Proteobacteria, Actinobacteria, Ascomycota, and Basidiomycota were the dominant bacterial and fungal communities in A. muelleri seeds at different maturation stages. The KEGG and COG functional gene annotation results revealed that the seed samples during the three maturation stages had higher KO functional diversity than the seed coat samples, and the COG functional diversity of the green and red seed samples was also significantly higher than that of the seed coat samples. At different maturation stages, microbial functional genes involved in energy production and conversion as well as carbon fixation were enriched in the A. muelleri seed coats, while microbial functional genes involved in signal transduction mechanisms, amino acid transport and metabolism, carbohydrate metabolism, and lipid metabolism were more highly expressed in the seeds. Moreover, in the middle to late stages of seed maturation, the microbial functional genes involved in the biosynthesis of resistant compounds such as phenols, flavonoids, and alkaloids were significantly enriched to enhance the resistance and environmental adaptation of A. muelleri seeds. The results verified that the functions of the endophytic microbial communities change dynamically during A. muelleri seed maturation to adapt to the current needs of the host plant, which has significant implications for the exploration and utilization of functional microbial resources in A. muelleri seeds.},
}
@article {pmid39557257,
year = {2024},
author = {Dong, J and Wang, L and Bai, Y and Huang, X and Chen, C and Liu, Y},
title = {Study on the physicochemical properties and immune regulatory mechanism of polysaccharide fraction from Aronia Melanocarpa fruit.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {137696},
doi = {10.1016/j.ijbiomac.2024.137696},
pmid = {39557257},
issn = {1879-0003},
abstract = {Aronia Melanocarpa (Michx.) Elliott fruit has been extensively used in the food and medicinal fields. This study aimed to analyze the physicochemical properties of a polysaccharide fraction (AMP2) isolated from this fruit for the first time and investigated its immune regulatory mechanism. The physicochemical properties of AMP2 were determined using high-performance gel permeation chromatography, PMP derivatization-high performance liquid chromatography, Ultraviolet spectroscopy, and infrared spectroscopy. The metagenomic technology was applied to investigate the regulatory effects and mechanisms of AMP2 on the gut microbiota of immunosuppressed mice. The results showed that molecular weight of AMP2 was 83,444 Da, which was mainly composed of D-arabinose, D-xylose, D-mannose, D-rhamnose and d-glucose, and both β-type and α-type glycosidic bonds contained in its structure. AMP2 changed the composition of gut microbiota by increasing the number of beneficial and probiotic bacteria, thereby regulated the intestinal mucosal immune system of host. AMP2 improved intestinal immune system response and antimicrobial capacity through positive regulation of the NOD-like receptor signaling pathway and neutrophil extracellular trap formation. The results demonstrate the potential of AMP2 in immune regulation, providing a new perspective for its subsequent development and contributing to the development and application of related health foods.},
}
@article {pmid39557245,
year = {2024},
author = {Qin, X and Huang, W and Li, Q},
title = {Lignocellulose biodegradation to humic substances in cow manure-straw composting: Characterization of dissolved organic matter and microbial community succession.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {137758},
doi = {10.1016/j.ijbiomac.2024.137758},
pmid = {39557245},
issn = {1879-0003},
abstract = {Composting, a sustainable practice, facilitates the biodegradation of organic waste, notably lignocellulosic biomass, into value-added humic substances. Despite its potential, the application of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS) to characterize dissolved organic matter (DOM) for assessing the changes in maturity during cow manure-straw composting is underexplored. Furthermore, the link between these changes, microbial community succession, and the biochemical pathways of humus formation is seldom investigated. This study leveraged ESI FT-ICR MS and metagenomic analysis to elucidate the molecular changes in DOM, identified key microbes in humus formation, and traced the humus formation pathway during composting. The results highlighted the crucial role of microorganisms such as Thermobifida, Luteimonas, Ascomycota, and Chloroflexi in accelerating the breakdown and transformation of plant biopolymers. Large molecular nitrogen compounds from cow manure-straw were converted into unsaturated, aromatic oxygen compounds, which resemble humic substances in their chemical properties. The ESI FT-ICR MS data revealed that humus formation occurred through a series of reactions, including protein deamination, lignin delignification, and decarbonylation. This research offered new light on strategies to enhance the stabilization and humification of cow manure-straw composting, contributing to more effective composting processes.},
}
@article {pmid39557129,
year = {2024},
author = {Drane, K and Huerlimann, R and Jones, R and Whelan, A and Sheehan, M and Ariel, E and Kinobe, R},
title = {Concordance in molecular methods for detection of antimicrobial resistance: A cross sectional study of the influent to a wastewater plant.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107069},
doi = {10.1016/j.mimet.2024.107069},
pmid = {39557129},
issn = {1872-8359},
abstract = {Methods that are used to characterise microbiomes and antimicrobial resistance genes (ARGs) in wastewater are not standardised. We used shotgun metagenomic sequencing (SM-Seq), RNA sequencing (RNA-seq) and targeted qPCR to compare microbial and ARG diversity in the influent to a municipal wastewater treatment plant in Australia. ARGs were annotated with CARD-RGI and MEGARes databases, and bacterial diversity was characterised by 16S rRNA gene sequencing and SM-Seq, with species annotation in SILVA/GreenGenes databases or Kraken2 and the NCBI nucleotide database respectively. CARD and MEGARes identified evenly distributed ARG profiles but MEGARes detected a richer array of ARGs (richness = 475 vs 320). Qualitatively, ARGs encoding for aminoglycoside, macrolide-lincosamide-streptogramin and multidrug resistance were the most abundant in all examined databases. RNA-seq detected only 32 % of ARGs identified by SM-Seq, but there was concordance in the qualitative identification of aminoglycoside, macrolide-lincosamide, phenicol, sulfonamide and multidrug resistance by SM-Seq and RNA-seq. qPCR confirmed the detection of some ARGs, including OXA, VEB and EREB, that were identified by SM-Seq and RNA-seq in the influent. For bacteria, SM-Seq or 16S rRNA gene sequencing were equally effective in population profiling at phyla or class level. However, SM-Seq identified a significantly higher species richness (richness = 15,000 vs 3750). These results demonstrate that SM-Seq with gene annotation in CARD and MEGARes are equally sufficient for surveillance of antimicrobial resistance in wastewater. For more precise ARG identification and quantification however, MEGARes presented a better resolution. The functionality of detected ARGs was not confirmed, but general agreement on the putative phenotypic resistance profile by antimicrobial class was observed between RNA-Seq and SM-Seq.},
}
@article {pmid39557097,
year = {2024},
author = {Zheng, X and Li, Y and Xu, J and Zhang, Q and Zhang, Y},
title = {Characterization of three novel dimethyl disulfide degrading bacteria and their potential degradation pathways.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131833},
doi = {10.1016/j.biortech.2024.131833},
pmid = {39557097},
issn = {1873-2976},
abstract = {Dimethyl disulfide (DMDS) is an odor compound characterized by the lowest olfactory threshold and high toxicity. It is indispensable to explore the bacteria with high resistance and degradation efficiency to DMDS. Acinetobacter lwoffii, Pseudomonas mendocina, and Myroides odoratus were isolated from kitchen waste. After 6 days of individual treatment, the removal rates were 34.22 %, 40.95 %, and 41.94 % respectively. The DMDS metabolic pathways based on metagenomic assays were discovered to be incomplete due to the insufficient annotation of some key genes in the current database. Following 3 days of treatment with bacterial consortia at ratios of 5:1 for A. lwoffii C2/ M. odoratus C7 and 1:1:1 for the three strains achieved 100 % DMDS removal. Additionally, the consortia reduced hydrogen sulfide (H2S) and dimethyl sulfide (DMS).This discovery broadens the spectrum of bacteria exhibiting high tolerance and efficient degradation of DMDS, with significant implications for DMDS removal and odor treatment.},
}
@article {pmid39557096,
year = {2024},
author = {Tan, Z and Chen, W and Wei, X and Qiu, Z and Zhuang, W and Zhang, B and Xie, J and Lin, Y and Ren, Y and Preis, S and Wei, C and Zhu, S},
title = {Virus-bacterium interaction involved in element cycles in biological treatment of coking wastewater.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131839},
doi = {10.1016/j.biortech.2024.131839},
pmid = {39557096},
issn = {1873-2976},
abstract = {Although prokaryotic microbes in coking wastewater (CWW) treatment have been comprehensively studied, the ecological functions of viruses remain unclear. A full-scale CWW biological treatment AOHO combination was studied for the virus-bacterium interactions involved in element cycles by metaviromics, metagenomics and physicochemical characteristics. Results showed the unique viromic profile with Cirlivirales and Petitvirales as the dominant viruses infecting functional bacteria hosts. The auxiliary metabolic genes (AMGs) focused on element cycles, including metabolisms of carbon (fadA), nitrogen (glnA), sulfur (mddA and cysK) and phosphorus (phoH). Other AMGs were involved in toxic tolerance of hosts, improving their cell membrane and wall robustness, antioxidant, DNA repair and cobalamin biosynthesis. Vice versa, the bloomed host provided fitness advantages for viruses. Dissolved oxygen was found to be the key factor shaping the distributions of viral community and AMGs. Summarizing, the study exposed the mutual virus-bacterium interaction in the AOHO combination providing stable treatment efficiency.},
}
@article {pmid39556808,
year = {2024},
author = {Roshandel, D and Spiliopoulou, A and McGurnaghan, SJ and Iakovliev, A and Lipschutz, D and Hayward, C and Bull, SB and Klein, BEK and Lee, KE and Kinney, GL and Rewers, M and Costacou, T and Miller, RG and McKeigue, PM and Paterson, AD and Colhoun, HM},
title = {Genetics of C-peptide and Age at Diagnosis in Type 1 Diabetes.},
journal = {Diabetes},
volume = {},
number = {},
pages = {},
doi = {10.2337/db24-0340},
pmid = {39556808},
issn = {1939-327X},
abstract = {Identified genetic loci for C-peptide and age at diagnosis (AAD) in individuals with type 1 diabetes (T1D) explain only a small proportion of their variation. Here, we aimed to perform large metagenome-wide association studies (GWAS) of C-peptide and AAD in T1D; and to identify the HLA allele/haplotypes associated with C-peptide and AAD. 7,252 and 7,923 European individuals with T1D were included in C-peptide and AAD GWAS, respectively. HLA-DQB1*06:02 which is strongly protective against T1D was associated with higher C-peptide. HLA-DQB1*03:02, HLADRB1*03:01 and HLA-A*24:02 which increase T1D risk were independently associated with younger AAD. HLA-DR3-DR4 haplotype combination, the strongest T1D susceptibility factor, was associated with younger AAD. Outside HLA region, rs115673528 on Chr5 (GABRG2) was associated with C-peptide, and an indel, rs111970692, on Chr15 within CTSH, a known T1D locus, was associated with AAD. Genetically predicted CTSH expression, methylation and protein levels were associated with AAD; Mendelian randomization analysis suggested that higher levels of procathepsin H reduce AAD. In conclusion, some HLA allele/haplotypes associated with T1D also contribute to variability of C-peptide and AAD. Outside HLA, T1D loci are generally not associated with C-peptide or AAD. CTSH could be a potential therapeutic target to delay development/progression of type 1 diabetes.},
}
@article {pmid39555414,
year = {2024},
author = {Wang, J and Liu, H and Kou, X and Zhang, Y and Wang, Y and Chen, C and Xiang, Z and Wang, X and Su, C and Liu, Y},
title = {Toxic effects of DEHP and MEHP on gut-liver axis in rats via intestinal flora and metabolomics.},
journal = {iScience},
volume = {27},
number = {11},
pages = {111135},
pmid = {39555414},
issn = {2589-0042},
abstract = {Di (2-ethylhexyl) phthalate (DEHP) is an environmental endocrine disruptor and commonly used as a plasticizer. Exposure to DEHP and its active metabolite mono-2-ethylhexyl phthalate (MEHP) can lead to adverse health consequences; however, the toxic mechanism is remains unclear. In this research, male and female rats were exposed to DEHP and MEHP by oral gavage for 60 consecutive days. Pathological analysis revealed that DEHP and MEHP exposure could affect liver, heart, kidney, and testis tissues, as well as alter biochemical indicators. Metagenomics (16S rRNA gene sequencing) analysis indicated that DEHP and MEHP could reduce the diversity and alter the composition of the gut microbiota. Toxic exposure also affected the levels of short chain fatty acids (SCFAs), with noticeable variations between genders. Metabolomic analysis revealed that DEHP and MEHP could influence bile acids, amino acids, hormones, and lipids. These results demonstrate that exposure to DEHP and MEHP can induce toxicity in rats via the gut-liver axis.},
}
@article {pmid39555017,
year = {2024},
author = {Wang, S and Su, LY and Chen, J and Tian, Y and Zhou, H},
title = {Integrated multi-omics profiling highlights the diet-gut-brain axis in low-calorie diets promoted novelty-seeking behavior.},
journal = {Current research in food science},
volume = {9},
number = {},
pages = {100897},
pmid = {39555017},
issn = {2665-9271},
abstract = {The foods that we eat are closely linked to the development and function of neurophysiology, affecting mood, cognition, and mental health. Yet, it is not known whether and how dietary patterns affect brain function and mood. Here, we explored the impact of various diets on the behavior of mice. Low-calorie (LC) diet-fed mice exhibited increased novel exploratory behaviors, including novelty to new foods, objects, and environments. The host transcriptome sequencing showed an increase of Areg in the cerebral cortex of mice fed with LC, and IMPC showed that Areg knock-out mice exhibited significantly decreased exploration of novel environments. According to the metagenomic sequencing results, a significant increase in the levels of s_Schaedlerella and s_1XD8-76 was observed after LC feeding. Integrated analysis of microbiota metabolites and host transcriptomics suggested that 68 differential metabolites in LC-fed mice were associated with upregulation of Areg expression. This study demonstrates the powerful impact of LC feeding on the restoration of gut microbiota and the improvement of novelty-seeking behavior. In addition, this study supports the idea that microbiota-associated metabolites can modulate host gene transcription, which provides a link between dietary patterns and their impact on the emotional and cognitive centers of the brain.},
}
@article {pmid39554614,
year = {2024},
author = {Liu, R and Qiao, X and Shi, Y and Peterson, CB and Bush, WS and Cominelli, F and Wang, M and Zhang, L},
title = {Constructing phylogenetic trees for microbiome data analysis: A mini-review.},
journal = {Computational and structural biotechnology journal},
volume = {23},
number = {},
pages = {3859-3868},
pmid = {39554614},
issn = {2001-0370},
abstract = {As next-generation sequencing technologies advance rapidly and the cost of metagenomic sequencing continues to decrease, researchers now face an unprecedented volume of microbiome data. This surge has stimulated the development of scalable microbiome data analysis methods and necessitated the incorporation of phylogenetic information into microbiome analysis for improved accuracy. Tools for constructing phylogenetic trees from 16S rRNA sequencing data are well-established, as the highly conserved regions of the 16S gene are limited, simplifying the identification of marker genes. In contrast, metagenomic and whole genome shotgun (WGS) sequencing involve sequencing from random fragments of the entire gene, making identification of consistent marker genes challenging owing to the vast diversity of genomic regions, resulting in a scarcity of robust tools for constructing phylogenetic trees. Although bacterial sequence tree construction tools exist for upstream bioinformatics, many downstream researchers-those integrating these trees into statistical models or machine learning-are either unaware of these tools or find them difficult to use due to the steep learning curve of processing raw sequences. This is compounded by the fact that public datasets often lack phylogenetic trees, providing only abundance tables and taxonomic classifications. To address this, we present a comprehensive review of phylogenetic tree construction techniques for microbiome data (16S rRNA or whole-genome shotgun sequencing). We outline the strengths and limitations of current methods, offering expert insights and step-by-step guidance to make these tools more accessible and widely applicable in quantitative microbiome data analysis.},
}
@article {pmid39553288,
year = {2024},
author = {Chowdhury, S and Kullberg, RFJ and Haak, BW and Duran, C and Earny, VA and Eshwara, VK and Lawley, TD and Wiersinga, WJ and Mukhopadhyay, C},
title = {Gut Microbiome in Human Melioidosis: Composition and Resistome Dynamics from Diagnosis to Discovery.},
journal = {Open forum infectious diseases},
volume = {11},
number = {11},
pages = {ofae654},
pmid = {39553288},
issn = {2328-8957},
abstract = {BACKGROUND: Melioidosis, attributable to the soil-dwelling bacterium Burkholderia pseudomallei, stands as a paramount global health challenge, necessitating extended courses of antibiotics. While murine studies identified the gut microbiota as a modulator of bacterial dissemination during melioidosis, the human intestinal microbiota during melioidosis remains uncharacterized. Here, we characterized gut microbiota composition and antimicrobial resistance (AMR) genes at diagnosis, during treatment, and postdischarge for melioidosis. We hypothesized that the gut microbiota of melioidosis patients would be extensively distorted.<br><br>METHODS: In this prospective observational cohort, stool samples of patients with culture-confirmed melioidosis admitted to a tertiary care hospital in India were collected at diagnosis, 14 days after diagnosis, or discharge (whichever occurred first) and at 6 months postinfection. Family members or neighbors served as community controls. The gut microbiota and resistome were profiled by shotgun metagenomic sequencing.<br><br>RESULTS: We longitudinally analyzed the gut microbiota of 70 fecal samples from 28 patients and 16 community controls. At diagnosis, the gut microbiota of patients differed from that of controls, characterized by high abundances of potentially pathogenic bacteria, a loss of butyrate-producing bacteria, and higher levels of AMR genes. Microbiota composition and resistome remained different from community controls at 6 months, driven by total antibiotic exposure. During hospitalization, gut microbiota profiles were associated with secondary Klebsiella pneumoniae infections.<br><br>CONCLUSIONS: This first study on gut microbiota composition and resistome in human melioidosis showed extensive disruptions during hospitalization, with limited signs of restoration 6 months postinfection. Given the adverse outcomes linked with microbiome perturbations, limiting microbiota disruptions or using microbiota-restorative therapies (eg, butyrate-producing probiotics) may be beneficial.},
}
@article {pmid39552867,
year = {2024},
author = {Ma, R and Liu, Z and Zhang, L and Chen, C and Yuan, B and Luo, Y and Marcos, PJ and Tattevin, P and Zhang, W},
title = {Epidemiological characteristics of severe community-acquired pneumonia in children admitted to two tertiary hospitals in Shihezi, Xinjiang Region, China in 2023: a cross-sectional analysis.},
journal = {Journal of thoracic disease},
volume = {16},
number = {10},
pages = {6969-6982},
pmid = {39552867},
issn = {2072-1439},
abstract = {BACKGROUND: Severe community-acquired pneumonia (SCAP) in children is associated with high morbidity and mortality, and the data of epidemiological characteristics of SCAP in Shihezi area were inadequate. The main pathogens responsible for SCAP may vary dramatically according to the geographical area. We identified two tertiary hospitals with better medical level and the largest number of hospitalized children in Shihezi as sentinel hospitals. The primary purpose of the study is to cross-sectionally summarize the epidemiological characteristics of SCAP in children admitted to hospitals in Shihezi, Xinjiang, China in 2023.<br><br>METHODS: SCAP was defined as involving the respiratory and other systems, accompanied by significant systemic toxic symptoms. We prospectively included all patients <15 years old who diagnosed with SCAP according to the SCAP diagnostic criteria. We enrolled all patients <15 years who were diagnosed with SCAP during the study period (January to December 2023), a total of 309 cases were included from two sentinel hospitals in Shihezi, Xinjiang, from January to December 2023. Basic information and clinical data were collected on a standardized questionnaire, and respiratory samples were obtained for the detection of 27 respiratory pathogens using a panel, targeted next-generation sequencing (t-NGS), and metagenomic next-generation sequencing (mNGS).<br><br>RESULTS: We enrolled 309 patients aged 1-14 years: 157 males (50.8%) and 152 females (49.2%). There were 45 infants (1 month to 1 year, 14.6%), 33 toddlers (>1-3 years, 10.7%), 121 preschool children (>3-7 years, 39.2%), and 110 school-age children (>7-14 years, 35.6%). Overall, the number of SCAP cases in spring was 39 (12.6%), in summer was 44 (14.2%), in autumn was 137 (44.3%), and in winter was 89 (28.8%). A total of 572 pathogens were detected in this study, primarily Mycoplasma pneumoniae (MP) (n=120, 21.0%), respiratory syncytial virus (RSV) (n=82 strains, 14.3%), and Streptococcus pneumoniae (SP) (n=67, 11.7%). MP was prevalent mainly during the cold season of autumn, with its detection starting from July and reaching a peak detection rate in November. By studying the interaction among 22 common respiratory pathogens, we found a strong negative correlation between MP and SP, yet the highest number of co-infected cases involved MP and SP. Seventy-six (63.3% of all MP) SCAP were identified as macrolide-resistant (all with mutations at the A2063G site). MP SCAP was associated with prolonged illness duration and fever spikes. We observed incidence of pediatric SCAP showed an inverse trend with PM2.5 level changes.<br><br>CONCLUSIONS: The most common pathogens responsible for SCAP in the Shihezi region in 2023 were MP, RSV, and SP. MP was the primary cause of SCAP in children, and increased risk of co-infections, and high prevalence of macrolides resistance-all related to mutations at the A2063G site. Early identification of SCAP pathogen epidemiological characteristics can reduce severe case occurrence.},
}
@article {pmid39552541,
year = {2024},
author = {Singh, CK and Sodhi, KK},
title = {Targeting bioinformatics tools to study the dissemination and spread of antibiotic resistant genes in the environment and clinical settings.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-19},
doi = {10.1080/1040841X.2024.2429603},
pmid = {39552541},
issn = {1549-7828},
abstract = {Antibiotic resistance has expanded as a result of the careless use of antibiotics in the medical field, the food industry, agriculture, and other industries. By means of genetic recombination between commensal and pathogenic bacteria, the microbes obtain antibiotic resistance genes (ARGs). In bacteria, horizontal gene transfer (HGT) is the main mechanism for acquiring ARGs. With the development of high-throughput sequencing, ARG sequence analysis is now feasible and widely available. Preventing the spread of AMR in the environment requires the implementation of ARGs mapping. The metagenomic technique, in particular, has helped in identifying antibiotic resistance within microbial communities. Due to the exponential growth of experimental and clinical data, significant investments in computer capacity, and advancements in algorithmic techniques, the application of machine learning (ML) algorithms to the problem of AMR has attracted increasing attention over the past five years. The review article sheds a light on the application of bioinformatics for the antibiotic resistance monitoring. The most advanced tool currently being employed to catalog the resistome of various habitats are metagenomics and metatranscriptomics. The future lies in the hands of artificial intelligence (AI) and machine learning (ML) methods, to predict and optimize the interaction of antibiotic-resistant compounds with target proteins.},
}
@article {pmid39552505,
year = {2024},
author = {Hiraoka, S and Ijichi, M and Takeshima, H and Kumagai, Y and Yang, CC and Makabe-Kobayashi, Y and Fukuda, H and Yoshizawa, S and Iwasaki, W and Kogure, K and Shiozaki, T},
title = {Probe Capture Enrichment Sequencing of amoA Genes Improves the Detection of Diverse Ammonia-Oxidising Archaeal and Bacterial Populations.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14042},
doi = {10.1111/1755-0998.14042},
pmid = {39552505},
issn = {1755-0998},
support = {JP19H04263//Japan Society for the Promotion of Science/ ; JP20K15444//Japan Society for the Promotion of Science/ ; JP21H03592//Japan Society for the Promotion of Science/ ; JP22H03716//Japan Society for the Promotion of Science/ ; JP22H04925//Japan Society for the Promotion of Science/ ; JP23H05411//Japan Society for the Promotion of Science/ ; JPMJCR11A3//Japan Science and Technology Agency/ ; JPMJCR19S2//Japan Science and Technology Agency/ ; JPMXD1521474594//Ministry of Education, Culture, Sports, Science and Technology/ ; },
abstract = {The ammonia monooxygenase subunit A (amoA) gene has been used to investigate the phylogenetic diversity, spatial distribution and activity of ammonia-oxidising archaeal (AOA) and bacterial (AOB), which contribute significantly to the nitrogen cycle in various ecosystems. Amplicon sequencing of amoA is a widely used method; however, it produces inaccurate results owing to the lack of a 'universal' primer set. Moreover, currently available primer sets suffer from amplification biases, which can lead to severe misinterpretation. Although shotgun metagenomic and metatranscriptomic analyses are alternative approaches without amplification bias, the low abundance of target genes in heterogeneous environmental DNA restricts a comprehensive analysis to a realisable sequencing depth. In this study, we developed a probe set and bioinformatics workflow for amoA enrichment sequencing using a hybridisation capture technique. Using metagenomic mock community samples, our approach effectively enriched amoA genes with low compositional changes, outperforming amplification and meta-omics sequencing analyses. Following the analysis of metatranscriptomic marine samples, we predicted 80 operational taxonomic units (OTUs) assigned to either AOA or AOB, of which 30 OTUs were unidentified using simple metatranscriptomic or amoA gene amplicon sequencing. Mapped read ratios to all the detected OTUs were significantly higher for the capture samples (50.4 ± 27.2%) than for non-capture samples (0.05 ± 0.02%), demonstrating the high enrichment efficiency of the method. The analysis also revealed the spatial diversity of AOA ecotypes with high sensitivity and phylogenetic resolution, which are difficult to examine using conventional approaches.},
}
@article {pmid39551951,
year = {2024},
author = {Yao, L and Devotta, H and Li, J and Lunjani, N and Sadlier, C and Lavelle, A and Albrich, WC and Walter, J and O'Toole, PW and O'Mahony, L},
title = {Dysrupted microbial tryptophan metabolism associates with SARS-CoV-2 acute inflammatory responses and long COVID.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2429754},
doi = {10.1080/19490976.2024.2429754},
pmid = {39551951},
issn = {1949-0984},
mesh = {Humans ; *Tryptophan/metabolism/blood ; *COVID-19/immunology/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; *SARS-CoV-2/immunology ; *Cytokines/blood/metabolism ; Middle Aged ; Aged ; *Feces/microbiology/virology ; Post-Acute COVID-19 Syndrome ; Indoles/metabolism ; Indoleacetic Acids/metabolism/blood ; Inflammation ; Adult ; Dysbiosis/microbiology ; },
abstract = {Protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and risk of long COVID has been associated with the depletion or over-abundance of specific taxa within the gut microbiome. However, the microbial mechanisms mediating these effects are not yet known. We hypothesized that altered microbial production of tryptophan and its downstream derivatives might contribute to inappropriate immune responses to viral infection. In patients hospitalized with COVID-19 (n = 172), serum levels of tryptophan and indole-3-propionate (IPA) negatively correlated with serum levels of many proinflammatory mediators (including C-reactive protein and Serum amyloid A), while C-glycosyltryptophan (C-Trp), indole-3-lactic acid (ILA) and indole-3-acetic acid (IAA) levels were positively correlated with levels of acute phase proteins, proinflammatory cytokines, alarmins and chemokines. A similar pattern was observed in long COVID patients (n = 20) where tryptophan and IPA were negatively associated with a large number of serum cytokines, while C-Trp and IAA were positively associated with circulating cytokine levels. Metagenomic analysis of the fecal microbiota showed the relative abundance of genes encoding the microbial enzymes required for tryptophan production (e.g. anthranilate synthase) and microbial tryptophan metabolism was significantly lower in patients hospitalized with COVID-19 (n = 380) compared to healthy controls (n = 270). Microbial tryptophan metabolites reduced innate cell proinflammatory responses to cytosolic DNA sensor Stimulator of interferon genes (STING), toll-like receptor (TLR)-3 and TLR-4 stimulation in vitro, while IL-10 secretion was enhanced. Microbial tryptophan metabolites also modified ex vivo human lymphocyte responses by limiting the production of TH1 and TH17 associated cytokines, while enhancing secretion of IL-22. These data suggest that lower levels of tryptophan production and tryptophan metabolism by gut microbes may increase the risk of severe and chronic outcomes to SARS-CoV-2 infection due to impaired innate and adaptive responses to infection. Screening patients for lower-level microbiome capacity for tryptophan metabolism may help identify at-risk individuals.},
}
@article {pmid39551884,
year = {2024},
author = {Mamo, Z and Abera, S and Tafesse, M},
title = {Taxonomic and functional profiling of microbial community in municipal solid waste dumpsite.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {40},
number = {12},
pages = {384},
pmid = {39551884},
issn = {1573-0972},
support = {EN-1/17-1/18//Addis Ababa Science and Technology University/ ; },
mesh = {*Solid Waste ; *Bacteria/classification/genetics/metabolism ; *Waste Disposal Facilities ; *Microbiota ; *Metagenomics ; Phylogeny ; Refuse Disposal ; Biodegradation, Environmental ; Drug Resistance, Microbial/genetics ; Soil Microbiology ; },
abstract = {Understanding the microbial ecology of landfills is crucial for improving waste management strategies and utilizing the potential of these microbial communities for biotechnological applications. This study aimed to conduct a comprehensive taxonomic and functional profiling of the microbial community present in the Addis Ababa municipal solid waste dumpsite using a shotgun metagenomics sequencing approach. The taxonomic analysis of the sample revealed the significant presence of bacteria, with the Actinomycetota (56%), Pseudomonadota (23%), Bacillota (3%), and Chloroflexota (3%) phyla being particularly abundant. The most abundant KEGG categories were carbohydrates metabolism, membrane transport, signal transduction, and amino acid metabolism. The biodegradation and metabolism of xenobiotics, as well as terpenoids and polyketides, were also prevalent. Moreover, the Comprehensive Antibiotic Resistance Database (CARD) identified 52 antibiotic resistance gene (ARG) subtypes belonging to 14 different drug classes, with the highest abundances observed for glycopeptide, phosphonic acid, and multidrug resistance genes. Actinomycetota was the dominant phylum harboring ARGs, followed by Pseudomonadota and Chloroflexota. This study offers valuable insights into the taxonomic and functional diversity of the microbial community in the Addis Ababa municipal solid waste dumpsite. It sheds light on the widespread presence of metabolically versatile microbes, antibiotic resistance genes, mobile genetic elements, and pathogenic bacteria. This understanding can contribute to the creation of efficient waste management strategies and the investigation of possible biotechnological uses for these microbial communities.},
}
@article {pmid39551377,
year = {2024},
author = {Siew, SW and Khairi, MHF and Hamid, NA and Asras, MFF and Ahmad, HF},
title = {Shallow Shotgun Sequencing of Healthcare Waste Reveals Plastic-Eating Bacteria with Broad-Spectrum Antibiotic Resistance Genes.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125330},
doi = {10.1016/j.envpol.2024.125330},
pmid = {39551377},
issn = {1873-6424},
abstract = {The burgeoning crises of antimicrobial resistance and plastic pollution are converging in healthcare settings, presenting a complex challenge to global health. This study investigates the microbial populations in healthcare waste to understand the extent of antimicrobial resistance and the potential for plastic degradation by bacteria. Our metagenomic analysis, using both amplicon and shallow shotgun sequencing, provided a comprehensive view of the taxonomic diversity and functional capacity of the microbial consortia. The viable bacteria in healthcare waste samples were analyzed employing full-length 16S rRNA sequencing, revealing a diverse bacterial community dominated by Firmicutes and Proteobacteria phyla. Notably, Proteus mirabilis VFC3/3 and Pseudomonas sp. VFA2/3 were detected, while Stenotrophomonas maltophilia VFV3/2 surfaced as the predominant species, holding implications for the spread of hospital-acquired infections and antimicrobial resistance. Antibiotic susceptibility testing identified multidrug-resistant strains conferring antimicrobial genes, including the broad-spectrum antibiotic carbapenem, underscoring the critical need for improved waste management and infection control measures. Remarkably, we found genes linked to the breakdown of plastic that encoded for enzymes of the esterase, depolymerase, and oxidoreductase classes. This suggests that specific bacteria found in medical waste may be able to reduce the amount of plastic pollution that comes from biological and medical waste. The information is helpful in formulating strategies to counter the combined problems of environmental pollution and antibiotic resistance. This study emphasises the importance of monitoring microbial communities in hospital waste in order to influence waste management procedures and public health policy. The findings highlight the need for a multidisciplinary approach to mitigate the risks associated with antimicrobial resistance and plastic waste, especially in hospital settings where they intersect most acutely.},
}
@article {pmid39551356,
year = {2024},
author = {Lalli, MK and Salo, TEI and Hakola, L and Knip, M and Virtanen, SM and Vatanen, T},
title = {Associations between dietary fibers and gut microbiome composition in the EDIA longitudinal infant cohort.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajcnut.2024.11.011},
pmid = {39551356},
issn = {1938-3207},
abstract = {BACKGROUND: The infant gut microbiome undergoes rapid changes in the first year of life, supporting normal development and long-term health. While diet shapes this process, the role of fibers in complementary foods on gut microbiome maturation is poorly understood.<br><br>OBJECTIVES: We explored how the transition from human milk to fibers in complementary foods shapes the taxonomic and functional maturation of the gut microbiome within the first year of life.<br><br>METHODS: We assessed the longitudinal and cross-sectional development of infant gut microbiomes (N=68 infants) and metabolomes (N=33 infants) using linear mixed models to uncover their associations to dietary fibers and their food sources. Fiber intakes were assessed with 3-day food records (months 3,6,9,12) relying on CODEX-compliant fiber fraction values, and questionnaires tracked the overall complementary food introduction. Bacterial species were identified and quantified via MetaPhlAn2 from metagenomic data, and metabolomic profiles were obtained using four LC-MS methods.<br><br>RESULTS: We identified 176 complementary food fiber-bacterial species associations. First plant-based fibers associated to microbiota compositions similar to breastfeeding, and further associated with aromatic amino acid metabolites, including 5-hydroxyindoleacetic acid (Total dietary fiber - Complementary foods (g) - &#x3b2;=3.50, CI 2.48-4.52, p=6.53x10-5). Distinct fibers from different food categories showed unique associations with specific bacterial taxa. Key species such as Faecalibacterium prausnitznii, associated with oat fibers (g/MJ, &#x3b2;=2.18, CI 1.36-2.84, p=6.12x10-6), reflective of maturing microbial communities. Fiber intake during weaning associated with shifts in metabolite profiles, including immunomodulatory metabolites, with fiber effects observed in a source- and timing-dependent manner, implicated in gradual microbiome diversification.<br><br>CONCLUSIONS: Introducing complementary dietary fibers during the weaning period supports gut microbiome diversification and stabilization. Even minor dietary variations showed significant associations with microbial taxa and functions from the onset of weaning, highlighting the importance of infant dietary recommendations that support the gut microbiome maturation during early life.<br><br>Clinicaltrials.gov Identifier: NCT01735123. Date of registration: November 24, 2012. https://www.<br><br>CLINICALTRIALS: gov/ct2/show/NCT01735123.},
}
@article {pmid39551294,
year = {2024},
author = {Zhang, G and Du, J and Zhang, C and Zhao, Z and Chen, Y and Liu, M and Chen, J and Fan, G and Ma, L and Li, S and Liu, K},
title = {Identification of a PET hydrolytic enzyme from the human gut microbiome unveils potential plastic biodegradation in human digestive tract.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {137732},
doi = {10.1016/j.ijbiomac.2024.137732},
pmid = {39551294},
issn = {1879-0003},
abstract = {Widespread use of polyethylene terephthalate (PET) plastics and their recycling challenges have led to substantial accumulation of PET wastes in global environments, with inevitable consequences for their entry into the food chains. Recent studies have increasingly documented the ingestion of microplastics by humans through food and beverages. However, the fate of these microplastics within the gastrointestinal tract, particularly the role of the human gut microbiota, remains inadequately understood. To address this knowledge gap, we employed a bioinformatics workflow integrated with functional verification to investigate the PET digestion/degradation capabilities of intestinal microorganisms. This approach identified a novel PET hydrolase-HGMP01 from the human gut metagenome, which exhibits the capacity to hydrolyze PET nanoparticles. Moreover, comprehensive exploration for HGMP01 homologues in the human gut metagenome and metatranscriptome unveil their distribution in diverse intestinal microorganisms. This study provides biochemical evidence for an unforeseen role of human gut microbiome in plastic digestion, thus holding substantial implications for human health.},
}
@article {pmid39551110,
year = {2024},
author = {Adenaike, AS and Akpan, U and Oyedun, IO and Adewole, FA and Agbaje, M and Olusanya, OM and Arowosegbe, MO and Ikeobi, CON},
title = {Gut microbial composition differs among FUNAAB Alpha broiler chicken genotypes raised in a tropical environment.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107126},
doi = {10.1016/j.micpath.2024.107126},
pmid = {39551110},
issn = {1096-1208},
abstract = {The gut microbiota of FUNAAB Alpha chickens plays a crucial role in determining their overall health and performance. Understanding the various types and diversity of microbiota in the gut of different genotypes of chickens is crucial for enhancing their well-being, productivity, and disease resistance. This study employed 16S rRNA and metagenomics analysis to examine the gut bacteria of three genotypes of FUNAAB Alpha broiler chickens, namely Naked neck, Frizzle, and Normal feather. There were three phyla observed in the three genotypes: Bacteroidetes, Actinobacteria, and Firmicutes. Through the utilisation of 16S rRNA sequencing, we successfully identified and categorised the various microbiota present within the gastrointestinal tract. Our study revealed notable variations in the composition and quantity of microbiota across the three genotypes, suggesting that each genotype possesses a distinct collection of gut bacteria. A wide range of microbiological diversity was observed within the community. Interestingly, the Normal feather chicken exhibited a greater number of operational taxonomic units (OTUs) compared to the Naked neck and Frizzle feather chicken. This study presents significant findings regarding the ceacal microbiota of FUNAAB Alpha chickens, emphasising the variations observed among different genotypes. It is crucial to study composition-modification techniques to enhance host health and performance, as well as to control zoonotic pathogens that can contaminate poultry products and threaten consumers' health.},
}
@article {pmid39550955,
year = {2024},
author = {Liu, S and Cao, J and Yu, J and Jian, M and Zou, L},
title = {Microplastics exacerbate the ecological risk of antibiotic resistance genes in wetland ecosystem.},
journal = {Journal of environmental management},
volume = {372},
number = {},
pages = {123359},
doi = {10.1016/j.jenvman.2024.123359},
pmid = {39550955},
issn = {1095-8630},
abstract = {Wetlands are vital components of the global ecosystem, significantly influencing the retention and dissemination of microplastics (MPs) and antibiotic resistance genes (ARGs). However, the effects of different types of MPs on the environmental dynamics of ARGs within these ecosystems remain poorly understood. This study focused on the distribution and composition of ARGs associated with two primary types of MPs-polyethylene and polypropylene-within the Poyang Lake wetland, the largest freshwater lake in China, utilizing metagenomic analysis. The findings demonstrated that the bacterial communities and ARG profiles in the plastisphere were markedly distinct from those in the surrounding water. Specifically, thirteen opportunistic pathogens and forty subtypes of ARGs, primarily related to multidrug, bacitracin, and β-lactam resistance, were identified in the plastisphere. Notably, polyethylene exhibited four times more specific ARG subtypes than polypropylene. Procrustes analysis combined with network analysis indicated a lack of strong correlation between ARG abundance and bacterial populations, suggesting potential horizontal transfer of ARGs within the microbiota of the plastisphere. Additionally, three novel and functional β-lactamase genes were identified within this environment. This investigation highlights the role of MPs as reservoirs for ARGs, facilitating their exchange and posing risks to both ecological integrity and human health, thereby underscoring the need for increased attention in future research efforts.},
}
@article {pmid39550949,
year = {2024},
author = {Wu, ZL and Shi, WJ and Zhang, L and Xia, ZY and Gou, M and Sun, ZY and Tang, YQ},
title = {Investigating the robustness of microbial communities in municipal sludge anaerobic digestion under organic loading rate disturbance.},
journal = {Journal of environmental management},
volume = {372},
number = {},
pages = {123326},
doi = {10.1016/j.jenvman.2024.123326},
pmid = {39550949},
issn = {1095-8630},
abstract = {Anaerobic digestion (AD) frequently encounters disturbances due to variations in organic loading rates (OLRs), which can result in the failure of the sludge treatment process. However, there is a lack of comprehensive studies on the robustness of AD systems against OLR disturbances and the underlying mechanisms. In this study, the responses of reactor performance and active microbial communities in mesophilic AD were investigated and compared under conditions of OLR shock and OLR fluctuation. Statistical analysis confirmed that all reactors recovered from both types of OLR disturbance, indicating both functional and structural robustness of the mesophilic community. Based on metagenomics and metatranscriptomics analyses, it was observed that high diversity within the microbial community led to functional redundancy, which appears to be a key mechanism contributing to the robustness against OLR disturbances. Additionally, for the first time, the potential metabolic diversity of aerobic autotrophy bacteria in AD reactors was identified, including their roles in the utilization of glucose and acetate. Furthermore, the analysis of topological properties within the microbial interaction network was conducted, and the robustness of the community network was verified through the application of random node deletion attacks. The findings from this study provide valuable information for the effective regulation of microbial communities and the design of practical AD systems.},
}
@article {pmid39550746,
year = {2024},
author = {Karaca, C and Takcı, HAM},
title = {Role of gut microbiome in developing necrotizing enterocolitis.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {39550746},
issn = {1874-9356},
support = {21-13192//Kilis 7 Aral&#x131;k University of Research Project Committee/ ; },
abstract = {Necrotizing enterocolitis (NEC) is one of the most devastating intestinal diseases observed in preterm in the first days of life. Researchers have recently focused on potential predictive biomarkers for early and concomitant diagnoses. Thus, we inquired about the linkage of intestinal dysbiosis, one of the most important factors in NEC development to the gut microbiota. In this study, the systematic differences in the bacterial composition between neonates affected by NEC and healthy newborns were highlighted by metagenomic analysis. The next-generation sequencing of the V3-V4 variable region of the 16S rRNA gene and gene-specific qPCR analyzed the untargeted gut microbiota. Total bacteria, total and fecal coliform loads in stool samples with NEC were higher than control. OTU-level relative abundances of NEC infant was characterized by Firmicutes and Bacteroidetes at phylum levels. At the genus level, NEC stool was identified by the lack of Klebsiella and the presence of Roseburia, Blautia, and Parasutterella. Finally, Clostridium fessum was the predominant species of Clostridium genus in disease and healthy specimens at the species level, whereas Clostridium jeddahitimonense was at NEC diagnosis. Despite a strong relationship between pathophysiology and characterization of gut microbiota at a clinical diagnosis of NEC, our results emphasize the broad difficulty in identifying potential biomarkers.},
}
@article {pmid39550535,
year = {2024},
author = {Yadav, A and Subramanian, S},
title = {HiFiBGC: an ensemble approach for improved biosynthetic gene cluster detection in PacBio HiFi-read metagenomes.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1096},
pmid = {39550535},
issn = {1471-2164},
support = {Department of Biotechnology//Department of Biotechnology, Ministry of Science and Technology, India/ ; OLP0175//CSIR - Institute of Microbial Technology/ ; },
mesh = {*Multigene Family ; *Metagenome ; Metagenomics/methods ; Workflow ; High-Throughput Nucleotide Sequencing/methods ; Software ; Computational Biology/methods ; },
abstract = {BACKGROUND: Microbes produce diverse bioactive natural products with applications in fields such as medicine and agriculture. In their genomes, these natural products are encoded by physically clustered genes known as biosynthetic gene clusters (BGCs). Genome and metagenome sequencing advances have enabled high-throughput identification of BGCs as a promising avenue for natural product discovery. BGC mining from (meta)genomes using in silico tools has allowed access to a vast diversity of potentially novel natural products. However, a fundamental limitation has been the ability to assemble complete BGCs, especially from complex metagenomes. With their fragmented assemblies, short-read technologies struggle to recover complete BGCs, such as the long and repetitive nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS). Recent advances in long-read sequencing, such as the High Fidelity (HiFi) technology from PacBio, have reduced this limitation and can help retrieve both accurate and complete BGCs from metagenomes, warranting improvement in the existing BGC identification approach for better utilization of HiFi data.<br><br>RESULTS: Here, we present HiFiBGC, a command-line-based workflow to identify BGCs in PacBio HiFi metagenomes. HiFiBGC leverages an ensemble of assemblies from three HiFi-tailored metagenome assemblers and the reads not represented in these assemblies. Based on our analyses of four HiFi metagenomic datasets from four different environments, we show that HiFiBGC identifies, on average, 78% more BGCs than the top-performing single-assembler-based method. This increase is due to HiFiBGC's ensemble assembly approach, which improves recovery by 25%, as well as from the inclusion of mostly fragmented BGCs identified in the unmapped reads.<br><br>CONCLUSIONS: HiFiBGC is a computational workflow for identifying BGCs in long-read HiFi metagenomes, implemented majorly using Python programming language and workflow manager Snakemake. HiFiBGC is available on GitHub at https://github.com/ay-amityadav/HiFiBGC under the MIT license. The code related to the figures and analyses presented in the manuscript is available at https://github.com/ay-amityadav/HiFiBGC_analyses .},
}
@article {pmid39550371,
year = {2024},
author = {Yang, JX and Peng, Y and Yu, QY and Yang, JJ and Zhang, YH and Zhang, HY and Adams, CA and Willing, CE and Wang, C and Li, QS and Han, XG and Gao, C},
title = {Gene horizontal transfers and functional diversity negatively correlated with bacterial taxonomic diversity along a nitrogen gradient.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {128},
pmid = {39550371},
issn = {2055-5008},
mesh = {*Gene Transfer, Horizontal ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Nitrogen/metabolism ; *Phylogeny ; *Biodiversity ; Metagenome ; DNA, Bacterial/genetics ; Soil Microbiology ; },
abstract = {Horizontal gene transfer (HGT) mediated diversification is a critical force driving evolutionary and ecological processes. However, how HGT might relate to anthropogenic activity such as nitrogen addition, and its subsequent effect on functional diversity and cooccurrence networks remain unknown. Here we approach this knowledge gap by blending bacterial 16S rRNA gene amplicon and shotgun metagenomes from a platform of cessation of nitrogen additions and continuous nitrogen additions. We found that bacterial HGT events, functional genes, and virus diversities increased whereas bacterial taxonomic diversity decreased by nitrogen additions, resulting in a counterintuitive strong negative association between bacterial taxonomic and functional diversities. Nitrogen additions, especially the ceased one, complexified the cooccurrence network by increasing the contribution of vitamin B12 auxotrophic Acidobacteria, indicating cross-feeding. These findings advance our perceptions of the causes and consequences of the diversification process in community ecology.},
}
@article {pmid39550223,
year = {2024},
author = {Bosilj, M and Suljič, A and Zakotnik, S and Slunečko, J and Kogoj, R and Korva, M},
title = {MetaAll: integrative bioinformatics workflow for analysing clinical metagenomic data.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {6},
pages = {},
doi = {10.1093/bib/bbae597},
pmid = {39550223},
issn = {1477-4054},
support = {J3-50101//Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana and Slovenian Research and Innovation Agency/ ; },
mesh = {Humans ; *Metagenomics/methods ; *Computational Biology/methods ; *Workflow ; COVID-19/virology/diagnosis ; SARS-CoV-2/genetics ; Metagenome ; Software ; },
abstract = {Over the past decade, there have been many improvements in the field of metagenomics, including sequencing technologies, advances in bioinformatics and the development of reference databases, but a one-size-fits-all sequencing and bioinformatics pipeline does not yet seem achievable. In this study, we address the bioinformatics part of the analysis by combining three methods into a three-step workflow that increases the sensitivity and specificity of clinical metagenomics and improves pathogen detection. The individual tools are combined into a user-friendly workflow suitable for analysing short paired-end (PE) and long reads from metagenomics datasets-MetaAll. To demonstrate the applicability of the developed workflow, four complicated clinical cases with different disease presentations and multiple samples collected from different biological sites as well as the CAMI Clinical pathogen detection challenge dataset were used. MetaAll was able to identify putative pathogens in all but one case. In this case, however, traditional microbiological diagnostics were also unsuccessful. In addition, co-infection with Haemophilus influenzae and Human rhinovirus C54 was detected in case 1 and co-infection with SARS-Cov-2 and Influenza A virus (FluA) subtype H3N2 was detected in case 3. In case 2, in which conventional diagnostics could not find a pathogen, mNGS pointed to Klebsiella pneumoniae as the suspected pathogen. Finally, this study demonstrated the importance of combining read classification, contig validation and targeted reference mapping for more reliable detection of infectious agents in clinical metagenome samples.},
}
@article {pmid39549663,
year = {2024},
author = {Méndez, A and Maisto, F and Pavlović, J and Rusková, M and Pangallo, D and Sanmartín, P},
title = {Microbiome shifts elicited by ornamental lighting of granite facades identified by MinION sequencing.},
journal = {Journal of photochemistry and photobiology. B, Biology},
volume = {261},
number = {},
pages = {113065},
doi = {10.1016/j.jphotobiol.2024.113065},
pmid = {39549663},
issn = {1873-2682},
abstract = {Night-time outdoor illumination in combination with natural sunlight can influence the visible phototrophic colonizers (mainly algae) growing on stone facades; however, the effects on the microbiome (invisible to the naked eye) are not clear. The presence of stone-dwelling microbes, such as bacteria, diatoms, fungi, viruses and archaea, drives further biological colonization, which may exacerbate the biodeterioration of substrates. Considering the microbiome is therefore important for conservation of the built heritage. The impact of the following types of lighting on the relative abundance and diversity of the microbiome on granite ashlars was evaluated in a year-long outdoor pilot study: no lighting; lighting with a metal halide lamp (a traditional lighting system currently used to illuminate monuments); and lighting with a novel LED lamp (an environmentally sound prototype lamp with a biostatic effect, halting biological colonization by phototrophs, currently under trial). Culturable fractions of microbiome and whole-genome sequencing by metabarcoding with Oxford Nanopore Sequencing (MinION) was conducted for bacteria and fungi in order to complement both community characterization strategies. In addition, the possible biodeteriorative profiles of the isolated strains, relative to calcium carbonate precipitation/solubilisation and iron oxidation/reduction, were investigated by plate assays. Alpha and beta diversity indexes were also determined, along with the abundance of biocide and antibiotic resistance genes. Culture-dependent microbiological analysis failed to properly show changes in community composition, for which metagenomic approaches like MinION are better suited. Thus, MinION analysis identified shifts in the granite microbiome elicited by ornamental lighting. The novel LED lamp with the biostatic effect on phototrophs caused an increase in the diversity of bacteria and fungi. In this case, the microbiome was more similar to that in the unlit samples. In the samples illuminated by the metal halide lamp, dominance of bacteria was favoured and the presence of fungi was negligible.},
}
@article {pmid39549623,
year = {2024},
author = {White, CA and Antell, EH and Schwartz, SL and Lawrence, JE and Keren, R and Zhou, L and Yu, K and Zhuang, WQ and Alvarez-Cohen, L},
title = {Life history strategies determine response to SRT driven crash in anammox bioreactors.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122727},
doi = {10.1016/j.watres.2024.122727},
pmid = {39549623},
issn = {1879-2448},
abstract = {Anaerobic ammonium oxidation (anammox) is a biological process often applied in wastewater treatment plants for nitrogen removal from highly concentrated side-stream effluents from anaerobic digesters. However, they are vulnerable to process instability prompted by operational shocks and microbial community imbalances, resulting in lengthy recovery times. These issues are further compounded by a lack of understanding of how sustained press disturbances influence the microbial ecology of the system. Here we investigate the response and recovery of an anammox membrane bioreactor to a solids retention time (SRT)-induced reactor crash using 16S rRNA gene and shotgun metagenomic sequencing. We observed a strong selection of bacterial groups based on reproduction strategies, with the Orders Rhodospirillales and Sphingobacteriales increasing from 1.0 % and 11.9 % prior to the crash to 31.9 % and 18.1 % during the crash respectively. The Orders Brocadiales and Anaerolineales decreased from 17.3 % and 28.3 % to 7.3 % and 1.4 % over the same time period, respectively. Metagenomic and metatranscriptomic analyses revealed differential crash responses in metabolically distinct groups of bacteria, with increased expression of genes for extracellular carbohydrate active enzymes, peptidases and membrane transporters. Following the crash, the reactor recovered to its prior state of nitrogen removal performance and pathway analysis demonstrated increased expression of genes related to exopolysaccharide biosynthesis and quorum sensing during the reactor recovery period. This study highlights the effects of reactor perturbations on microbial community dynamics in anammox bioreactors and provides insight into potential recovery mechanisms from severe disturbance.},
}
@article {pmid39549575,
year = {2024},
author = {Ma, R and Peng, L and Tang, R and Jiang, T and Chang, J and Li, G and Wang, J and Yang, Y and Yuan, J},
title = {Bioaerosol emission characteristics and potential risks during composting: Focus on pathogens and antimicrobial resistance.},
journal = {Journal of hazardous materials},
volume = {481},
number = {},
pages = {136466},
doi = {10.1016/j.jhazmat.2024.136466},
pmid = {39549575},
issn = {1873-3336},
abstract = {In this study, we analyzed bioaerosol emission characteristics and potential risks of antimicrobial resistance (AMR) during composting using the impaction culture method and metagenomic sequencing. The results showed that the highly saturated water vapor in the emission gas mitigated particulate matter emission during the thermophilic period. About the bioaerosols, the airborne aerobic bacterial emissions were suppressed as composting enters the mature period, and the airborne fungi are usually present as single-cell or small-cell aggregates (< 3.3 µm). In addition, the microbial community structure in bioaerosols was stable and independent of composting time. Most importantly, the PM2.5 in bioaerosols contained large amounts of antibiotic resistance genes (ARGs), potential pathogens, and multidrug resistant pathogens, which were diverse and present in high concentrations. Among them, ARGs concentrations encoding 21 antibiotics ranged from - 4.50 to 0.70 ppm/m[3] (Log10 ARGs). Among the 89 potential human pathogens detected, Escherichia coli, Salmonella enterica, Klebsiella pneumoniae, and Staphylococcus aureus were the only culturable potentially multidrug resistant pathogens carrying multiple ARGs encoding resistance at high concentrations (- 0.57 to 1.15 ppm/m[3] (Log10 ARGs)), and were more likely to persist and multiply in oligotrophic environments. Our findings indicate that composting technology can transfer AMR from solid compost to gas phase and increase the risk of AMR transmission.},
}
@article {pmid39549023,
year = {2024},
author = {Xiang, J and Chai, N and Li, L and Hao, X and Linghu, E},
title = {Alterations of Gut Microbiome in Patients with Colorectal Advanced Adenoma by Metagenomic Analyses.},
journal = {The Turkish journal of gastroenterology : the official journal of Turkish Society of Gastroenterology},
volume = {35},
number = {11},
pages = {859-868},
doi = {10.5152/tjg.2024.24294},
pmid = {39549023},
issn = {2148-5607},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/microbiology/pathology ; Female ; Male ; *Adenoma/microbiology/pathology ; Middle Aged ; *Dysbiosis/microbiology ; *Feces/microbiology ; *Metagenomics/methods ; Case-Control Studies ; Aged ; Tryptophan/metabolism ; },
abstract = {BACKGROUND/AIMS: Colorectal cancer (CRC) is one of the deadliest cancers worldwide, mostly arising from adenomatous polyps. Mounting evidence has demonstrated that changes in the gut microbiome play key roles in CRC progression, while quite few studies focused on the altered microbiota architecture of advanced adenoma (AA), a crucial precancerous stage of CRC. Thus, we aimed to investigate the microbial profiles of AA patients.<br><br>MATERIALS AND METHODS: Fecal samples were collected from 26 AA patients and 26 age- and sex-matched normal controls (NC), and analyzed by shotgun metagenomic sequencing.<br><br>RESULTS: Gut microbial dysbiosis was observed in AA patients with lower alpha diversity. Advanced adenoma was characterized by an increased Bacillota/Bacteroidota ratio and higher Pseudomonadota levels compared to normal individuals. Linear discriminant analysis effect size (LEfSe) analysis was performed and identified 14 microbiota with significantly different abundance levels between AA and NC groups. Functional analysis revealed that tryptophan metabolism was upregulated in AA. Correspondingly, the expressions of gut microbes implicated in tryptophan metabolism also changed, including Akkermansia muciniphila, Bacteroides ovatus, Clostridium sporogenes, and Limosilactobacillus reuteri. The microbial network suggested that AA exhibited decreased correlation complexity, with Escherichia coli and Enterobacteriaceae unclassified harboring the strongest connectivity. A diagnostic model consisting of 3 microbial species was established based on random forest, yielding an area under the curve (AUC) of 0.799.<br><br>CONCLUSION: Our study profiled the alterations of the gut microbiome in AA patients, which may enrich the knowledge of microbial signatures along with colorectal tumorigenesis and provide promising biomarkers for AA diagnosis.},
}
@article {pmid39548565,
year = {2024},
author = {Grønbæk, IMB and Mollerup, S and Halkjær, SI and Paulsen, SJ and Pinholt, M and Westh, H and Petersen, AM},
title = {Faecal sample storage without ethanol for up to 24 h followed by freezing performs better than storage with ethanol for shotgun metagenomic microbiome analysis in patients with inflammatory and non-inflammatory intestinal diseases and healthy controls.},
journal = {BMC research notes},
volume = {17},
number = {1},
pages = {340},
pmid = {39548565},
issn = {1756-0500},
mesh = {Humans ; *Feces/microbiology ; *Ethanol ; *Gastrointestinal Microbiome/genetics ; *Specimen Handling/methods ; *Freezing ; Male ; Adult ; *Inflammatory Bowel Diseases/microbiology ; Female ; Metagenomics/methods ; Middle Aged ; Metagenome ; Case-Control Studies ; },
abstract = {OBJECTIVE: The influence of different faecal collection methods on metagenomic analyses remains under discussion, and there is no general agreement on which collection method is preferable for gut microbiome research. We compared faecal samples collected in tubes without preservatives with those containing 10 mL of 96% ethanol for gut microbiome research when the timeframe from defecation to freezing at - 80 °C was up to 24 h. We aimed to compare the collection methods on faeces from participants with inflammatory and non-inflammatory gastrointestinal disorders and healthy controls to investigate the most suitable method when considering data yield, human fraction of sequencing reads, and ease of use. We also examined the faecal sample homogeneity.<br><br>RESULTS: Faeces collected in tubes without preservatives resulted in more sequencing reads compared to faeces collected in tubes with 96% ethanol and were also easier to handle. The human fraction of total reads in faeces collected in ethanol from participants with inflammatory bowel disease was higher than all other samples. DNA extraction and sequencing from two different locations in the same faecal sample gave similar results and showed sample homogeneity.},
}
@article {pmid39548381,
year = {2024},
author = {Ke, Y and Jiang, Y and Yuan, Y and Chen, Y and Huang, J and Huang, C},
title = {Eosinophilic gastrointestinal diseases with overall gastrointestinal tract causing liver abscess in an older patient: a case report and literature review.},
journal = {BMC geriatrics},
volume = {24},
number = {1},
pages = {945},
pmid = {39548381},
issn = {1471-2318},
mesh = {Humans ; Aged ; Male ; *Eosinophilia/complications/diagnosis ; *Liver Abscess/complications/diagnosis ; *Klebsiella pneumoniae/isolation &amp; purification ; *Enteritis/complications/diagnosis/microbiology ; *Klebsiella Infections/complications/diagnosis ; Gastritis/diagnosis/complications/microbiology ; Gastrointestinal Diseases/diagnosis/complications ; },
abstract = {BACKGROUND: Eosinophilic gastrointestinal diseases are the rare gastrointestinal disorders. To our knowledge, there have been no reports of eosinophilic gastrointestinal diseases with overall gastrointestinal tract involvement causing liver abscess in an older patient.<br><br>CASE PRESENTATION: We report a 68-year-old man with eosinophilic gastrointestinal disease with overall gastrointestinal tract involvement. He was admitted with suspected acute gastroenteritis, and histological examination showed eosinophilic infiltration accompanied by liver abscess. The collected pus was tested for Metagenomics Next-Generation Sequencing and confirmed the presence of Klebsiella pneumoniae.<br><br>CONCLUSIONS: We conducted a literature review on the complications of eosinophilic gastrointestinal diseases and discussed how eosinophilic gastrointestinal diseases lead to liver abscess caused by Klebsiella pneumoniae.},
}
@article {pmid39547567,
year = {2024},
author = {Chen, G and Wang, R and Ying, L and Eheneden, I and Ren, H and Sun, M},
title = {Sulfamethoxazole removal in nitrifying membrane aerated biofilms: Physiological responses and antibiotic resistance genes.},
journal = {Environmental research},
volume = {},
number = {},
pages = {120365},
doi = {10.1016/j.envres.2024.120365},
pmid = {39547567},
issn = {1096-0953},
abstract = {Efficient removal of ammonia nitrogen and sulfamethoxazole (SMX) from wastewater has become increasingly critical due to their detrimental effects on aquatic ecosystems and public health. This study aimed to investigate the nitrogen transformation and SMX removal in a membrane aerated biofilm reactor (MABR) under different SMX concentrations (0 ∼ 200 μg·L[-1]) with a nitrifying membrane bioreactor (MBR) as a control. Results suggested that SMX removal in MABR was better than that of MBR with SMX addition (50 ∼ 200 μg·L[-1]). Membrane aerated biofilms tended to secrete more extracellular polymeric substances (EPS) and generate less antioxidant enzymes in response to SMX stress when compared with nitrifying sludge in MBR. Metagenomic analysis indicated that distinct succession of microbial community was observed in both systems after SMX addition, and the relative abundance of nitrifying bacteria (Nitrosomonas, Nitrospira, and Nitrobacter) evidently decreased under SMX concentration of 200 μg·L[-1]. The proliferation of predominant antibiotic resistance gene (ARG) sul2 was suppressed more obviously in MABR than that in MBR. Thus, this study provided extensive insights into the advantages of nitrifying MABR in simultaneous removal of ammonium and antibiotics with less risk of associated ARGs spread.},
}
@article {pmid39547561,
year = {2024},
author = {Xia, C and Cheng, W and Ren, M and Zhu, Y},
title = {Chromium(VI) and Nitrate Removal from Groundwater Using Biochar-Assisted Zero Valent Iron Autotrophic Bioreduction: Enhancing Electron Transfer Efficiency and Reducing EPS Accumulation.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125313},
doi = {10.1016/j.envpol.2024.125313},
pmid = {39547561},
issn = {1873-6424},
abstract = {Current strategies primarily utilize heterotrophic or mixotrophic bioreduction for the simultaneous removal of Cr(VI) and NO3[-] from groundwater. However, given the oligotrophic nature of groundwater, autotrophic bioreduction could be more appropriate, though it remains notably underdeveloped. Here, an autotrophic bioreduction technology utilizing biochar (BC)-assisted zero valent iron (ZVI) is proposed. The pyrolysis temperature of BC was optimized to enhance electron transfer efficiency and reduce extracellular polymeric substances (EPS) accumulation. BC500, with the superior electron transfer capabilities, was the most effective. After an 11-week period, the ZVI+BC500 biotic column still achieved 100% removal efficiency for Cr(VI) and 93.37±0.33% for NO3[-], with initial concentrations of 26 mg/L and 50 mg/L, respectively. Its performance significantly surpasses that of ZVI alone, effectively reducing the interference of Cr(VI) on denitrification. The presence of quinone and phenolic compounds in BC500, serving as electron-accepting and electron-donating groups, improves the efficiency of electron transfer between ZVI and microbes. Metagenomic analysis showed an increase in the growth of autotrophic bacteria such as Hydrogenophaga spp. and Rhodanobacter denitrificans, and heterotrophic bacteria including Arenimonas daejeonensis and Chryseobacterium shandongense. The promotion facilitates the expression of genes associated with Cr(VI) reduction (chrR, nemA) and denitrification (narG, nirS). BC500 also enhanced EPS production, which facilitates the adsorption and reduction of Cr(VI), mitigating its inhibitory effects on denitrification. Notably, in the ZVI+BC500 biotic column, the accumulated EPS primarily consists of loosely bound EPS rather than tightly bound EPS, potentially reducing the risk of pore clogging during in-situ groundwater treatment.},
}
@article {pmid39547283,
year = {2024},
author = {Zelasko, S and Swaney, MH and Sandstrom, S and Lee, KE and Dixon, J and Riley, C and Watson, L and Godfrey, JJ and Ledrowski, N and Rey, F and Safdar, N and Seroogy, CM and Gern, JE and Kalan, L and Currie, C},
title = {Early-life Upper Airway Microbiota are Associated with Decreased Lower Respiratory Tract Infections.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2024.11.008},
pmid = {39547283},
issn = {1097-6825},
abstract = {Microbial interactions mediating colonization resistance play key roles within the human microbiome, shaping susceptibility to infection from birth. To gain insight into microbiome-mediated defenses and respiratory pathogen colonization dynamics, we sequenced and analyzed nasal (n=229) and oral (n=210) microbiomes with associated health/environmental data from our Wisconsin Infant Study Cohort at age 24-months. Participants with early-life lower respiratory tract infection (LRTI) were more likely to be formula-fed, attend daycare, and experience wheezing. Shotgun metagenomic sequencing with detection of viral and bacterial respiratory pathogens revealed nasal microbiome composition to associate with prior LRTI - namely lower alpha diversity, depletion of Prevotella, and enrichment of Moraxella catarrhalis including drug-resistant strains. Prevotella originating from healthy microbiomes had higher biosynthetic gene cluster abundance and exhibited contact-independent inhibition of M. catarrhalis, suggesting interbacterial competition impacts nasal pathogen colonization. This work advances understanding of protective host-microbial interactions occurring in airway microbiomes that alter infection susceptibility in early-life.},
}
@article {pmid39547006,
year = {2024},
author = {Nakanishi, H and Takada, A and Yoneyama, K and Kodama, S and Sakai, K and Saito, K},
title = {The utility of drowning site inference through metagenomic diatom analysis.},
journal = {Legal medicine (Tokyo, Japan)},
volume = {71},
number = {},
pages = {102548},
doi = {10.1016/j.legalmed.2024.102548},
pmid = {39547006},
issn = {1873-4162},
abstract = {The diatom test is one of the methods used to diagnose drowning in forensic autopsies. Metagenomic diatom analysis may reveal where a drowning occurred. We evaluated whether metagenomic diatom analysis could be used to infer waters, watersheds, and geographic locations using 166 water samples from 64 locations (freshwater: 55; seawater: 9). Principal component analysis (PCA) in all samples revealed no specific clusters for waters or watersheds. In one river, the three samples at the same site generally tended to be in close clusters, but there were some cases where the three sites were far from each other. The precise geographic location could thus not be reliably identified. However, PCA of data from dams, lakes, and retention basins revealed sites with independent clusters, suggesting unique diatom compositions. Diatoms of seawater were not detected in freshwater. The high number of Actinoptychus, Chaetoceros, and Skeletonema detected in seawater samples suggested that they are useful for seawater identification. This method required only 2 mL of water; it suggests that this method can be applied to actual samples. In summary, it was difficult to infer the geographic location and waters or watersheds, but the freshwater/seawater distinction could be easily made, and depending on the application, it may be useful in forensic science practice.},
}
@article {pmid39546167,
year = {2024},
author = {Rajeev, M and Cho, JC},
title = {Rhodobacteraceae are Prevalent and Ecologically Crucial Bacterial Members in Marine Biofloc Aquaculture.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
pmid = {39546167},
issn = {1976-3794},
abstract = {Bioflocs are microbial aggregates primarily composed of heterotrophic bacteria that play essential ecological roles in maintaining animal health, gut microbiota, and water quality in biofloc aquaculture systems. Despite the global adoption of biofloc aquaculture for shrimp and fish cultivation, our understanding of biofloc microbiota-particularly the dominant bacterial members and their ecological functions-remains limited. In this study, we employed integrated metataxonomic and metagenomic approaches to demonstrate that the family Rhodobacteraceae of Alphaproteobacteria consistently dominates the biofloc microbiota and plays essential ecological roles. We first analyzed a comprehensive metataxonomic dataset consisting of 200 16S rRNA gene amplicons collected across three Asian countries: South Korea, China, and Vietnam. Taxonomic investigation identified Rhodobacteraceae as the dominant and consistent bacterial members across the datasets. The predominance of this taxon was further validated through metagenomics approaches, including read taxonomy and read recruitment analyses. To explore the ecological roles of Rhodobacteraceae, we applied genome-centric metagenomics, reconstructing 45 metagenome-assembled genomes. Functional annotation of these genomes revealed that dominant Rhodobacteraceae genera, such as Marivita, Ruegeria, Dinoroseobacter, and Aliiroseovarius, are involved in vital ecological processes, including complex carbohydrate degradation, aerobic denitrification, assimilatory nitrate reduction, ammonium assimilation, and sulfur oxidation. Overall, our study reveals that the common practice of carbohydrate addition in biofloc aquaculture systems fosters the growth of specific heterotrophic bacterial communities, particularly Rhodobacteraceae. These bacteria contribute to maintaining water quality by removing toxic nitrogen and sulfur compounds and enhance animal health by colonizing gut microbiota and exerting probiotic effects.},
}
@article {pmid39546027,
year = {2024},
author = {Khamespanah, E and Asad, S and Vanak, Z and Mehrshad, M},
title = {Niche-Aware Metagenomic Screening for Enzyme Methioninase Illuminates Its Contribution to Metabolic Syntrophy.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {141},
pmid = {39546027},
issn = {1432-184X},
mesh = {*Carbon-Sulfur Lyases/genetics/metabolism ; *Metagenomics ; *Phylogeny ; *Bacteria/genetics/classification/enzymology/isolation &amp; purification/metabolism ; Archaea/genetics/enzymology/classification ; Groundwater/microbiology ; Metagenome ; Seawater/microbiology ; },
abstract = {The single-step methioninase-mediated degradation of methionine (as a sulfur containing amino acid) is a reaction at the interface of carbon, nitrogen, sulfur, and methane metabolism in microbes. This enzyme also has therapeutic application due to its role in starving auxotrophic cancer cells. Applying our refined in silico screening pipeline on 33,469 publicly available genome assemblies and 1878 metagenome assembled genomes/single-cell amplified genomes from brackish waters of the Caspian Sea and the Fennoscandian Shield deep groundwater resulted in recovering 1845 methioninases. The majority of recovered methioninases belong to representatives of phyla Proteobacteria (50%), Firmicutes (29%), and Firmicutes_A (13%). Prevalence of methioninase among anaerobic microbes and in the anoxic deep groundwater together with the relevance of its products for energy conservation in anaerobic metabolism highlights such environments as desirable targets for screening novel methioninases and resolving its contribution to microbial metabolism and interactions. Among archaea, majority of detected methioninases are from representatives of Methanosarcina that are able to use methanethiol, the sulfur containing product from methionine degradation, as a precursor for methanogenesis. Branching just outside these archaeal methioninases in the phylogenetic tree, we recovered three methioninases belonging to representatives of Patescibacteria reconstructed from deep groundwater metagenomes. We hypothesize that methioninase in Patescibacteria could contribute to their syntrophic interactions where their methanogenic partners/hosts benefit from the produced 2-oxobutyrate and methanethiol. Our results underscore the significance of accounting for specific ecological niche in screening for enzyme variates with desired characteristics. Finally, complementing of our findings with experimental validation of methioninase activity confirms the potential of our in silico screening in clarifying the peculiar ecological role of methioninase in anoxic environments.},
}
@article {pmid39543100,
year = {2024},
author = {Krinos, AI and Mars Brisbin, M and Hu, SK and Cohen, NR and Rynearson, TA and Follows, MJ and Schulz, F and Alexander, H},
title = {Missing microbial eukaryotes and misleading meta-omic conclusions.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9873},
pmid = {39543100},
issn = {2041-1723},
support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-SC0020347//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; },
mesh = {*Eukaryota/genetics/classification ; Phylogeny ; Databases, Genetic ; Cluster Analysis ; Metagenomics/methods ; },
abstract = {Meta-omics is commonly used for large-scale analyses of microbial eukaryotes, including species or taxonomic group distribution mapping, gene catalog construction, and inference on the functional roles and activities of microbial eukaryotes in situ. Here, we explore the potential pitfalls of common approaches to taxonomic annotation of protistan meta-omic datasets. We re-analyze three environmental datasets at three levels of taxonomic hierarchy in order to illustrate the crucial importance of database completeness and curation in enabling accurate environmental interpretation. We show that taxonomic membership of sequence clusters estimates community composition more accurately than returning exact sequence labels, and overlap between clusters can address database shortcomings. Clustering approaches can be applied to diverse environments while continuing to exploit the wealth of annotation data collated in databases, and selecting and evaluating these databases is a critical part of correctly annotating protistan taxonomy in environmental datasets. We argue that ongoing curation of genetic resources is crucial in accurately annotating protists in in situ meta-omic datasets. Moreover, we propose that precise taxonomic annotation of meta-omic data is a clustering problem rather than a feasible alignment problem.},
}
@article {pmid39545936,
year = {2024},
author = {Mechikoff, MA and Collins, JP and Golder, P and Ingersoll, CM and McGarry, RE and Lu, XJ and Gokden, A and Cuff, A and Webber, BJ and Wallace, AB and Steel, JJ and Wickiser, JK and Balboni, AL},
title = {Application of Pan-Viral Metagenomic Sequencing on United States Air Force Academy Wastewater to Uncover Potential Causes of Acute Gastroenteritis.},
journal = {Military medicine},
volume = {},
number = {},
pages = {},
doi = {10.1093/milmed/usae518},
pmid = {39545936},
issn = {1930-613X},
support = {//Air Force Office of Scientific Research/ ; //Defense Health Agency/ ; //Skoll Foundation/ ; //Air Force Office of Scientific Research/ ; //Defense Health Agency/ ; //Skoll Foundation/ ; },
abstract = {INTRODUCTION: Wastewater surveillance is an important technique to monitor public health and is being studied extensively for pandemic prevention, force health protection and readiness, and as a potential early warning system for chem-bio defense. Wastewater surveillance has traditionally relied on techniques such as quantitative PCR or targeted sequencing, both of which are microbe- or disease-specific tools. Newer pan-viral metagenomics strategies may provide higher specificity for pathogens of interest, resulting in a lower false negative rate and reduced sequencing of undesired background nucleic acids. One such system, VirCapSeq-VERT, has been developed to target all vertebrate virus pathogens; until recently, its application has been limited to clinical samples. The objective of this study was to use VirCapSeq-VERT to interrogate wastewater samples from the U.S. Air Force Academy (USAFA), Colorado Springs, Colorado, to determine its utility in assessing complex samples and its potential application in public health surveillance.<br><br>MATERIALS AND METHODS: Biweekly samples were analyzed from February 2022 through May 2023. Samples were collected from the wastewater treatment facility at USAFA before treatment and stored at -20&#x2009;&#xb0;C until total nucleic acid (tNA: DNA and RNA) extraction. tNA was then subject to the probe-based capture system, VirCapSeq, and run through a collection of public bioinformatics pipelines to identify captured viral pathogens and perform phylogenetic analysis. It was determined by the USAFA IRB that the study was non-human subject research and was deemed exempt.<br><br>RESULTS: In total, 68 families of viruses were identified, comprising thousands of individual strains. This study focused on viruses responsible for gastrointestinal dysfunction as a test of the use of the VirCapSeq-VERT to identify human pathogenic viruses within a complex and highly enriched biological sample. Four enteric viruses dominated the wastewater samples, with Adenoviridae most prevalent before the cadet winter recess (December 17, 2022-January 4, 2023) and Astroviridae most abundant thereafter.<br><br>CONCLUSION: Although gastroenteritis outbreaks at USAFA are commonly attributed to norovirus because of clinical presentation and the acute nature of the illness-often diagnosed and treated without confirmatory stool testing-this virus was not found in high prevalence in these wastewater samples. Among adenoviruses, F serotype 41 predominated, suggesting a role in gastrointestinal infections among the cadet population. Phylogenetic investigation of adenovirus and norovirus exposed common variants with seasonal distributions. These findings may prompt correlational studies to assess the clinical predictive capability of VirCapSeq-VERT and to determine the utility of wastewater monitoring as an outbreak early warning system.},
}
@article {pmid39545782,
year = {2024},
author = {Zepernick, BN and Hart, LN and Natwora, KE and Brown, KM and Obuya, JA and Olokotum, M and Okech, EO and Keating, NG and Lomeo, D and Tebbs, EJ and , and Sheik, CS and Sherman, DH and Dick, GJ and Wilhelm, SW and Drouillard, KG and Lawrence, T and Getabu, A and Owuor, B and Shitandi, A and Omondi, R and Njiru, J and Sitoki, L and Otiso, KM and McKay, RML and Bullerjahn, GS},
title = {Metagenomic sequencing of cyanobacterial-dominated Lake Victoria-an African Great Lake.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0079824},
doi = {10.1128/mra.00798-24},
pmid = {39545782},
issn = {2576-098X},
abstract = {We report 40 metagenomic libraries collected from the Winam Gulf of Lake Victoria during May-July of 2022-2023 and an additional eight opportunistic libraries from adjacent Lakes Simbi, Naivasha, and regional river systems. The sampling period captured cyanobacterial bloom events - shedding insight onto community composition and genomic potential.},
}
@article {pmid39545734,
year = {2024},
author = {Xu, T and Ni, Y and Li, H and Wu, S and Yan, S and Chen, L and Yu, Y and Wang, Y},
title = {Discovery and characterization of complete genomes of 38 head-tailed proviruses in four predominant phyla of archaea.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0049224},
doi = {10.1128/spectrum.00492-24},
pmid = {39545734},
issn = {2165-0497},
abstract = {Archaea play a significant role in natural ecosystems and the human body. Archaeal viruses exert a considerable influence on the structure and composition of archaeal communities and their associated ecological environments. The present study revealed the complete genomes of 38 archaeal head-tailed proviruses through comprehensive data mining. The hosts of these proviruses were identified as belonging to the following four dominant phyla: Halobacteriota, Thermoplasmatota, Thermoproteota, and Nanoarchaeota. In addition to the 14 proviruses of halophilic archaea related to the Graaviviridae family, the remaining proviruses exhibited limited genetic similarities to known (pro)viruses, suggesting the existence of 14 potential novel families. Of the 38 archaeal proviruses, 30 have the potential to lyse host cells. Eleven proviruses contain genes linked to antiviral defense mechanisms, including those involved in restriction modification (RM), clustered regularly interspaced short palindromic repeat (CRISPR)-associated (CRISPR-Cas) nucleases, defense island system associated with restriction-modification (DISARM), and DNA degradation (Dnd). Moreover, auxiliary metabolic genes were identified in the proviruses of Bathyarchaeia and Halobacteriota archaea, including those involved in carbohydrate and amino acid metabolism. Our findings indicate the diversity of archaeal viruses, their interactions with archaeal hosts, and their roles in the adaptation of the host.IMPORTANCEThe field of archaeal virology has seen a rapid expansion through the use of metagenomics, yet the diversity of these viruses remains largely uncharted. In this study, the complete genomes of 38 novel archaeal proviruses were identified for the following four dominant phyla: Halobacteriota, Thermoplasmatota, Thermoproteota, and Nanoarchaeota. Two families and six genera of Archaea were the first to be identified as hosts for viruses. The proviruses were found to contain diverse genes that were involved in distinct adaptation strategies of viruses to hosts. Our findings contribute to the expansion of the lineages of archaeal viruses and highlight their intricate interactions and essential roles in enabling host survival and adaptation to diverse environmental conditions.},
}
@article {pmid39545729,
year = {2024},
author = {Beaudry, MS and Bhuiyan, MIU and Glenn, TC},
title = {Enriching the future of public health microbiology with hybridization bait capture.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0006822},
doi = {10.1128/cmr.00068-22},
pmid = {39545729},
issn = {1098-6618},
abstract = {SUMMARYPublic health microbiology focuses on microorganisms and infectious agents that impact human health. For years, this field has relied on culture or molecular methods to investigate complex samples of public health importance. However, with the increase in accuracy and decrease in sequencing cost over the last decade, there has been a transition to the use of next-generation sequencing in public health microbiology. Nevertheless, many available sequencing methods (e.g., shotgun metagenomics and amplicon sequencing) do not work well in complex sample types, require deep sequencing, or have inherent biases associated with them. Hybridization bait capture, also known as target enrichment, brings in solutions for such limitations. It is an increasingly popular technique to simultaneously characterize many thousands of genetic elements while reducing the amount of sequencing needed (thereby reducing the sequencing costs). Here, we summarize the concept of hybridization bait capture for public health, reviewing a total of 35 bait sets designed in six key topic areas for public health microbiology [i.e., antimicrobial resistance (AMR), bacteria, fungi, parasites, vectors, and viruses], and compare hybridization bait capture to previously relied upon methods. Furthermore, we provide an in-depth comparison of the three most popular bait sets designed for AMR by evaluating each of them against three major AMR databases: Comprehensive Antibiotic Resistance Database, Microbial Ecology Group Antimicrobial Resistance Database, and Pathogenicity Island Database. Thus, this article provides a review of hybridization bait capture for public health microbiologists.},
}
@article {pmid39545702,
year = {2024},
author = {Zhang, M and Ma, L and Luo, J and Ren, T and Liu, S and Pan, L and Bao, Y and Li, F and Dai, Y and Pi, Z and Yue, H and Zheng, F},
title = {Low-Medium Polarity Ginsenosides from Wild Ginseng Improves Immunity by Activating the AhR/MAPK Pathway through Tryptophan Metabolism Driven by Gut Microbiota.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c06019},
pmid = {39545702},
issn = {1520-5118},
abstract = {The gut microbiota contribute significantly to the immune system. Low-medium polarity ginsenosides from wild ginseng (LWG) have potential immunomodulatory effects. However, how the LWG regulates gut microbiota to enhance immunity remains unclear. To explore the interaction between gut microbes and metabolites mediating LWG's immunomodulatory effects, this study examined LWG's impact on splenocytes and CTX-induced immunosuppressed mice. Metabolomic and metagenomic analyses were conducted in vivo to explore the mechanism by which LWG regulates gut microbiota to enhance immunity. In vitro data suggest that LWG at 4 μg/mL enhances the splenocyte activity. Furthermore, LWG effectively reduces symptoms in immunocompromised mice, including weight loss and intestinal mucosal damage. LWG alleviated gut microbiota disturbance, restored tryptophan metabolites (IA, IAA, and IPA), and significantly increased JNK, ERK, and p38MAPK protein levels, which were downstream of AhR. Our study demonstrated that LWG improves the immunity by reshaping gut microbiota, restoring intestinal mucosa, and boosting the gut microbiota-related metabolism of tryptophan to activate the AhR/MAPK pathway. This research offers new insights into the mechanism by which LWG regulates immune function.},
}
@article {pmid39545400,
year = {2024},
author = {Stern, DB and Raborn, RT and Lovett, SP and Boise, NR and Carasquilla, L and Enke, S and Radune, D and Woodruff, DL and Wahl, K and Rosovitz, MJ},
title = {Novel toxin biosynthetic gene cluster in harmful algal bloom-causing Heteroscytonema crispum: Insights into the origins of paralytic shellfish toxins.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae248},
pmid = {39545400},
issn = {1759-6653},
abstract = {Caused by both eukaryotic dinoflagellates and prokaryotic cyanobacteria, harmful algal blooms (HABs) are events of severe ecological, economic, and public health consequence, and their incidence has become more common of late. Despite coordinated research efforts to identify and characterize the genomes of HAB-causing organisms, the genomic basis and evolutionary origins of paralytic shellfish toxins (PSTs) produced by HABs remain at best incomplete. The PST saxitoxin has an especially complex genomic architecture and enigmatic phylogenetic distribution, spanning dinoflagellates and multiple cyanobacterial genera. Using filtration and extraction techniques to target the desired cyanobacteria from non-axenic culture, coupled with a combination of short and long read sequencing, we generated a reference-quality hybrid genome assembly for Heteroscytonema crispum UTEX LB 1556, a freshwater, PST-producing cyanobacterium thought to have the largest known genome in its phylum. We report a complete, novel biosynthetic gene cluster for the PST saxitoxin. Leveraging this biosynthetic gene cluster, we find support for the hypothesis that PST production has appeared in divergent Cyanobacteria lineages through widespread and repeated horizontal gene transfer. This work demonstrates the utility of long-read sequencing and metagenomic assembly toward advancing our understanding of PST biosynthetic gene cluster diversity and suggests a mechanism for the origin of PST biosynthetic genes.},
}
@article {pmid39544963,
year = {2024},
author = {Wong, HL and Bulzu, PA and Ghai, R and Chiriac, MC and Salcher, MM},
title = {Ubiquitous genome streamlined Acidobacteriota in freshwater environments.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae124},
pmid = {39544963},
issn = {2730-6151},
abstract = {Acidobacteriota are abundant in soil, peatlands, and sediments, but their ecology in freshwater environments remains understudied. UBA12189, an Acidobacteriota genus, is an uncultivated, genome-streamlined lineage with a small genome size found in aquatic environments where detailed genomic analyses are lacking. Here, we analyzed 66 MAGs of UBA12189 (including one complete genome) from freshwater lakes and rivers in Europe, North America, and Asia. UBA12189 has small genome sizes (<1.4 Mbp), low GC content, and a highly diverse pangenome. In freshwater lakes, this bacterial lineage is abundant from the surface waters (epilimnion) down to a 300-m depth (hypolimnion). UBA12189 appears to be free-living from CARD-FISH analysis. When compared to other genome-streamlined bacteria such as Nanopelagicales and Methylopumilus, genome reduction has caused UBA12189 to have a more limited metabolic repertoire in carbon, sulfur, and nitrogen metabolisms, limited numbers of membrane transporters, as well as a higher degree of auxotrophy for various amino acids, vitamins, and reduced sulfur. Despite having reduced genomes, UBA12189 encodes proteorhodopsin, complete biosynthesis pathways for heme and vitamin K2, cbb3-type cytochrome c oxidases, and heme-requiring enzymes. These genes may give a selective advantage during the genome streamlining process. We propose the new genus Acidiparvus, with two new species named "A. lacustris" and "A. fluvialis". Acidiparvus is the first described genome-streamlined lineage under the phylum Acidobacteriota, which is a free-living, slow-growing scavenger in freshwater environments.},
}
@article {pmid39544492,
year = {2024},
author = {Xiao, S and Zhou, W and Caldwell, R and Decker, S and Oh, J and Milstone, AM},
title = {Association of Neonatal and Maternal Nasal Microbiome Among Neonates in the Intensive Care Unit.},
journal = {Open forum infectious diseases},
volume = {11},
number = {11},
pages = {ofae644},
pmid = {39544492},
issn = {2328-8957},
abstract = {The neonatal nasal microbiota may help protect neonates in the neonatal intensive care unit from pathogen colonization and infection. This preliminary study characterized the biodiversity of nasal microbiota comparing neonates in the neonatal intensive care unit and their mothers, highlighting the potential of strain sharing between mother-neonate pairs.},
}
@article {pmid39544283,
year = {2024},
author = {Li, S and Fan, S and Ma, Y and Xia, C and Yan, Q},
title = {Influence of gender, age, and body mass index on the gut microbiota of individuals from South China.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1419884},
pmid = {39544283},
issn = {2235-2988},
abstract = {BACKGROUND: The symbiotic gut microbiota is pivotal for human health, with its composition linked to various diseases and metabolic disorders. Despite its significance, there remains a gap in systematically evaluating how host phenotypes, such as gender, age, and body mass index (BMI), influence gut microbiota.<br><br>We conducted an analysis of the gut microbiota of 185 Chinese adults based on whole-metagenome shotgun sequencing of fecal samples. Our investigation focused on assessing the effects of gender, age, and BMI on gut microbiota across three levels: diversity, gene/phylogenetic composition, and functional composition. Our findings suggest that these phenotypes have a minor impact on shaping the gut microbiome compared to enterotypes, they do not correlate significantly within- or between-sample diversity. We identified a substantial number of phenotype-associated genes and metagenomic linkage groups (MLGs), indicating variations in gut microflora composition. Specifically, we observed a decline in beneficial Firmicutes microbes, such as Eubacterium, Roseburia, Faecalibacterium and Ruminococcus spp., in both older individuals and those with higher BMI, while potentially harmful microbes like Erysipelotrichaceae, Subdoligranulum and Streptococcus spp. increased with age. Additionally, Blautia and Dorea spp. were found to increase with BMI, aligning with prior research. Surprisingly, individuals who were older or overweight exhibited a lack of Bacteroidetes, a dominant phylum in the human gut microbiota that includes opportunistic pathogens, while certain species of the well-known probiotics Bifidobacterium were enriched in these groups, suggesting a complex interplay of these bacteria warranting further investigation. Regarding gender, several gender-associated MLGs from Bacteroides, Parabacteroides, Clostridium and Akkermansia were enriched in females. Functional analysis revealed a multitude of phenotype-associated KEGG orthologs (KOs).<br><br>CONCLUSIONS/SIGNIFICANCE: Our study underscores the influence of gender, age, and BMI on gut metagenomes, affecting both phylogenetic and functional composition. However, further investigation is needed to elucidate the precise roles of these bacteria, including both pathogens and probiotics.},
}
@article {pmid39544279,
year = {2024},
author = {Hong, R and Lin, S and Zhang, S and Yi, Y and Li, L and Yang, H and Du, Z and Cao, X and Wu, W and Ren, R and Yao, X and Xie, B},
title = {Pathogen spectrum and microbiome in lower respiratory tract of patients with different pulmonary diseases based on metagenomic next-generation sequencing.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1320831},
pmid = {39544279},
issn = {2235-2988},
abstract = {INTRODUCTION: The homeostasis of the microbiome in lower respiratory tract is crucial in sustaining normal physiological functions of the lung. Different pulmonary diseases display varying degrees of microbiome imbalance; however, the specific variability and clinical significance of their microbiomes remain largely unexplored.<br><br>METHODS: In this study, we delineated the pathogen spectrum and commensal microorganisms in the lower respiratory tract of various pulmonary diseases using metagenomic sequencing. We analyzed the disparities and commonalities of the microbial features and examined their correlation with disease characteristics.<br><br>RESULTS: We observed distinct pathogen profiles and a diversity in lower airway microbiome in patients diagnosed with cancer, interstitial lung disease, bronchiectasis, common pneumonia, Nontuberculous mycobacteria (NTM) pneumonia, and severe pneumonia.<br><br>DISCUSSION: This study illustrates the utility of Metagenomic Next-generation Sequencing (mNGS) in identifying pathogens and analyzing the lower respiratory microbiome, which is important for understanding the microbiological aspect of pulmonary diseases and essential for their early and precise diagnosis.},
}
@article {pmid39544117,
year = {2024},
author = {Roslund, MI and Galitskaya, P and Saarenpää, M and Sinkkonen, A},
title = {Cultivar-dependent differences in plant bud microbiome and functional gene pathways in woody plants commonly used in urban green space.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovae110},
pmid = {39544117},
issn = {1472-765X},
abstract = {Plant richness and microbiota have been associated with plant health; hardly any studies have investigated how plant taxa differs in microbiota in the context of human health. We investigated the microbial differences in buds of 83 woody plant taxa used in urban green spaces in hemiboreal climate, using 16S rRNA and whole metagenome shotgun sequencing. Bud microbial community was the richest in Cotoneaster Nanshan and C. integerrimus, and Malus domestica cultivars 'Sandra' and 'Lobo' and poorest in Ribes glandulosum. Metagenomic shotgun sequencing of two M. domestica and four Ribes varieties confirmed differences in taxa in bud microbiota and indicated higher siderophore synthesis in Malus. Microbial richness, including bacteria, archaea and viruses, and functional richness of gene pathways was higher in Malus compared to Ribes. The ten most abundant amplicon sequence units, often referred as species, belonged to the phylum Proteobacteria. The differences between plant taxa were evident in classes Alpha- and Gammaproteobacteria, known for potential human health-benefits. Since environmental microbiota contributes to human microbiota and immunoregulation, horticultural cultivars hosting rich microbiota may have human health benefits. Further studies are needed to confirm the effectiveness of microbially-oriented plant selection in optimizing human microbiota and planetary health.},
}
@article {pmid39543873,
year = {2024},
author = {Saraswat, I and Goel, A},
title = {Therapeutic Modulation of the Microbiome in Oncology: Current Trends and Future Directions.},
journal = {Current pharmaceutical biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113892010353600241109132441},
pmid = {39543873},
issn = {1873-4316},
abstract = {Cancer is a predominant cause of mortality worldwide, necessitating the development of innovative therapeutic techniques. The human microbiome, particularly the gut microbiota, has become a significant element in cancer research owing to its essential role in sustaining health and influencing disease progression. This review examines the microbiome's makeup and essential functions, including immunological modulation and metabolic regulation, which may be evaluated using sophisticated methodologies such as metagenomics and 16S rRNA sequencing. The microbiome influences cancer development by promoting inflammation, modulating the immune system, and producing carcinogenic compounds. Dysbiosis, or microbial imbalance, can undermine the epithelial barrier and facilitate cancer. The microbiome influences chemotherapy and radiation results by modifying drug metabolism, either enhancing or reducing therapeutic efficacy and contributing to side effects and toxicity. Comprehending these intricate relationships emphasises the microbiome's significance in oncology and accentuates the possibility for microbiome-targeted therapeutics. Contemporary therapeutic approaches encompass the utilisation of probiotics and dietary components to regulate the microbiome, enhance treatment efficacy, and minimise unwanted effects. Advancements in research indicate that personalised microbiome-based interventions, have the potential to transform cancer therapy, by providing more effective and customised treatment alternatives. This study aims to provide a comprehensive analysis of the microbiome's influence on the onset and treatment of cancer, while emphasising current trends and future possibilities for therapeutic intervention.},
}
@article {pmid39543781,
year = {2024},
author = {Samuthpongtorn, C and Chan, AA and Ma, W and Wang, F and Nguyen, LH and Wang, DD and Okereke, OI and Huttenhower, C and Chan, AT and Mehta, RS},
title = {F. prausnitzii potentially modulates the association between citrus intake and depression.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {237},
pmid = {39543781},
issn = {2049-2618},
support = {U01 CA176726 to WW/CA/NCI NIH HHS/United States ; U01 CA176726 to WW/CA/NCI NIH HHS/United States ; U01 CA176726 to WW/CA/NCI NIH HHS/United States ; U01 CA176726 to WW/CA/NCI NIH HHS/United States ; U01 CA176726 to WW/CA/NCI NIH HHS/United States ; U01 CA176726 to WW/CA/NCI NIH HHS/United States ; U01 CA176726 to WW/NH/NIH HHS/United States ; U01 CA176726 to WW/NH/NIH HHS/United States ; U01 CA176726 to WW/NH/NIH HHS/United States ; R01MH091448/NH/NIH HHS/United States ; U01 CA176726 to WW/NH/NIH HHS/United States ; U01 CA176726 to WW/NH/NIH HHS/United States ; U01 CA176726 to WW/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: The gut microbiome modulates the effects of diet on host health, but it remains unclear which specific foods and microbial features interact to influence risk of depression. To understand this interplay, we leveraged decades of dietary and depression data from a longitudinal cohort of women (n = 32,427), along with fecal metagenomics and plasma metabolomics from a substudy (n = 207) nested in this cohort, as well as an independent validation cohort of men (n = 307).<br><br>RESULTS: We report that citrus intake and its components are prospectively associated with a lower risk of depression and altered abundance of 15 gut microbial species, including enriched Faecalibacterium prausnitzii. In turn, we found a lower abundance of F. prausnitzii and its metabolic pathway, S-adenosyl-L-methionine (SAM) cycle I in participants with depression. To explore causality, we found that lower SAM production by F. prausnitzii may decrease intestinal monoamine oxidase A gene expression implicated in serotonin and dopamine synthesis.<br><br>CONCLUSIONS: These data underscore the role of diet in the prevention of depression and offer a plausible explanation for how the intestinal microbiome modulates the influence of citrus on mental health. Video Abstract.},
}
@article {pmid39543780,
year = {2024},
author = {Zhao, XD and Gao, ZY and Peng, J and Konstantinidis, KT and Zhang, SY},
title = {Various microbial taxa couple arsenic transformation to nitrogen and carbon cycling in paddy soils.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {238},
pmid = {39543780},
issn = {2049-2618},
abstract = {BACKGROUND: Arsenic (As) metabolism pathways and their coupling to nitrogen (N) and carbon (C) cycling contribute to elemental biogeochemical cycling. However, how whole-microbial communities respond to As stress and which taxa are the predominant As-transforming bacteria or archaea in situ remains unclear. Hence, by constructing and applying ROCker profiles to precisely detect and quantify As oxidation (aioA, arxA) and reduction (arrA, arsC1, arsC2) genes in short-read metagenomic and metatranscriptomic datasets, we investigated the dominant microbial communities involved in arsenite (As(III)) oxidation and arsenate (As(V)) reduction and revealed their potential pathways for coupling As with N and C in situ in rice paddies.<br><br>RESULTS: Five ROCker models were constructed to quantify the abundance and transcriptional activity of short-read sequences encoding As oxidation (aioA and arxA) and reduction (arrA, arsC1, arsC2) genes in paddy soils. Our results revealed that the sub-communities carrying the aioA and arsC2 genes were predominantly responsible for As(III) oxidation and As(V) reduction, respectively. Moreover, a newly identified As(III) oxidation gene, arxA, was detected in genomes assigned to various phyla and showed significantly increased transcriptional activity with increasing soil pH, indicating its important role in As(III) oxidation in alkaline soils. The significant correlation of the transcriptional activities of aioA with the narG and nirK denitrification genes, of arxA with the napA and nirS denitrification genes and of arrA/arsC2 with the pmoA and mcrA genes implied the coupling of As(III) oxidation with denitrification and As(V) reduction with methane oxidation. Various microbial taxa including Burkholderiales, Desulfatiglandales, and Hyphomicrobiales (formerly Rhizobiales) are involved in the coupling of As with N and C metabolism processes. Moreover, these correlated As and N/C genes often co-occur in the same genome and exhibit greater transcriptional activity in paddy soils with As contamination than in those without contamination.<br><br>CONCLUSIONS: Our results revealed the comprehensive detection and typing of short-read sequences associated with As oxidation and reduction genes via custom-built ROCker models, and shed light on the various microbial taxa involved in the coupling of As and N and C metabolism in situ in paddy soils. The contribution of the arxA sub-communities to the coupling of As(III) oxidation with nitrate reduction and the arsC sub-communities to the coupling of As(V) reduction with methane oxidation expands our knowledge of the interrelationships among As, N, and C cycling in paddy soils. Video Abstract.},
}
@article {pmid39543707,
year = {2024},
author = {Wang, T and Ruan, Y and Xu, Q and Shen, Q and Ling, N and Vandenkoornhuyse, P},
title = {Effect of plant-derived microbial soil legacy in a grafting system-a turn for the better.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {234},
pmid = {39543707},
issn = {2049-2618},
abstract = {BACKGROUND: Plant-soil feedback arises from microbial legacies left by plants in the soil. Grafting is a common technique used to prevent yield declines in monocultures. Yet, our understanding of how grafting alters the composition of soil microbiota and how these changes affect subsequent crop performance remains limited. Our experiment involved monoculturing ungrafted and grafted watermelons to obtain conditioned soils, followed by growing the watermelons on the conditioned soils to investigate plant-soil feedback effects.<br><br>RESULTS: Ungrafted plants grew better in soil previously conditioned by a different plant (heterospecific soil) while grafted plants grew better in soil conditioned by the same plant (conspecific soil). We demonstrated experimentally that these differences in growth were linked to changes in microorganisms. Using a supervised machine learning algorithm, we showed that differences in the relative abundance of certain genera, such as Rhizobium, Chryseobacterium, Fusarium, and Aspergillus, significantly influenced the conspecific plant-soil feedback. Metabolomic analyses revealed that ungrafted plants in heterospecific soil enriched arginine biosynthesis, whereas grafted plants in conspecific soil increased sphingolipid metabolism. Elsewhere, the metagenome-assembled genomes (MAGs) of ungrafted plants identified in heterospecific soil include Chryseobacterium and Lysobacter, microorganisms having been prominently identified in earlier research as contributors to plant growth. Metabolic reconstruction revealed the putative ability of Chryseobacterium to convert D-glucono-1,5-lactone to gluconic acid, pointing to distinct disease-suppressive mechanisms and hence distinct microbial functional legacies between grafted and ungrafted plants.<br><br>CONCLUSIONS: Our findings show a deep impact of the soil microbial reservoir on plant growth and suggest the necessity to protect and improve this microbial community in agricultural soils. The work also suggests possibilities of optimizing microbiota-mediated benefits through grafting herein, a way that "engineered" soil microbial communities for better plant growth. Video Abstract.},
}
@article {pmid39543347,
year = {2024},
author = {Neo, O and Singh, N and Cazares, A},
title = {A river of resistant genes uncovered by metagenomics.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39543347},
issn = {1740-1534},
}
@article {pmid39543265,
year = {2024},
author = {Stevens, BR and Roesch, LFW},
title = {Interplay of human ABCC11 transporter gene variants with axillary skin microbiome functional genomics.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {28037},
pmid = {39543265},
issn = {2045-2322},
abstract = {The human armpit microbiome is metabolically entangled with skin cell physiology. This "meta-organism" symbiotic mutualism results in sweat either with or without odor (osmidrosis), depending on host ABCC11 gene haplotypes. Apocrine metabolism produces odorless S-glutathione conjugate that is transferred by ABCC11 transporters into secretory vesicles, deglutamylated to S-Cys-Gly-3M3SH thiol, and exuded to skin surface. An anthropogenic clade of skin bacteria then takes up the thiol and bioconverts it to malodorous 3-methyl-3-sulfanylhexan-1-ol (3M3SH). We hypothesized a familial meta-organism association of human ABCC11 gene non-synonymous SNP rs17822931 interplaying with skin microbiome 3M3SH biosynthesis. Subjects were genotyped for ABCC11 SNPs, and their haplotypes were correlated with axilla microbiome DNA sequencing profiles and predicted metagenome functions. A multigeneration family pedigree revealed a Mendelian autosomal recessive pattern: the C allele of ABCC11 correlated with bacterial Cys-S-conjugate β-lyase (PatB) gene known for Staphylococcus hominis biosynthesis of 3M3SH from human precursor; PatB was rescinded in hosts with homozygous TT alleles encoding ABCC11 loss-of-function mutation. We posit that a C allele encoding functional ABCC11 is key to delivering host conjugate precursors that shape heritable skin niche conditions favorable to harboring Staphylococcus having genomics of odor thiol production. This provides existential insights into human evolution and global regional population ancestries.},
}
@article {pmid39543167,
year = {2024},
author = {Sumithra, TG and Sharma, SRK and Suresh, G and Suja, G and Prasad, V and Gop, AP and Patil, PK and Gopalakrishnan, A},
title = {Gut microbes of a high-value marine fish, Snubnose Pompano (Trachinotus blochii) are resilient to therapeutic dosing of oxytetracycline.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {27949},
pmid = {39543167},
issn = {2045-2322},
support = {Grant No. CIBA/AINP-FH/2015-16//Indian Council of Agricultural Research/ ; BT/AAQ/3/SP28267/2018//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
abstract = {Trachinotus blochii is a high-value tropical mariculture species. The present study evaluated the gut microbial impact of therapeutic exposure (80 mg/day/kg biomass for 10 days) to oxytetracycline, the most common aquaculture antibiotic in T. blochii. The cultivable counts, α-diversity measures of taxonomic and functional metagenomics, microbial dysbiosis (MD) index, and microbial taxon abundances showed the resilience of gut microbiota at 16-26 days of treatment. A significant reduction in bacterial abundance, diversity measures, Firmicutes and Actinobacteria and an increase in γ-Proteobacteria was recorded on the 6th and 11th day of treatment. The increased metagenomic stress signatures, decreased beneficial bacterial abundances, decreased abundance of microbial pathways on energy metabolism, and MD index indicated short-term transient stress during the initial days of therapeutic withdrawal, warranting health management measures. Therapeutic exposure reduced the abundance of fish pathogens, including Vibrio spp., kanamycin and ampicillin-resistant bacteria. Strikingly, oxytetracycline treatment did not increase tetracycline-resistant bacterial counts and the predicted abundance of tetracycline resistance encoding genes in the gut, illustrating that therapeutic application would not pose a risk in the context of antimicrobial resistance in short term. Altogether, the present study provides a foundation for oxytetracycline treatment to develop suitable risk minimization tactics in sustainable aquaculture.},
}
@article {pmid39542977,
year = {2024},
author = {da Rosa, MT and da Luz Wallau, G and Loreto, ELS},
title = {A novel picorna-like virus in the flatworm Stenostomum leucops (Catenulida).},
journal = {Archives of virology},
volume = {169},
number = {12},
pages = {244},
pmid = {39542977},
issn = {1432-8798},
abstract = {We present the genome sequence and organization and evidence of persistence of a new picorna-like virus infecting the flatworm Stenostomum leucops. The complete genome sequence belongs to a virus with a positive single-stranded RNA genome with two open reading frames (ORFs) flanked by untranslated regions and a polyadenylated C-terminus. The ORFs encode proteins with conserved motifs typical of members of the order Picornavirales. Phylogenetic analysis confirmed membership in this viral order, and it was found to be closely related to viruses found in Biomphalaria (Mollusca) in France and a virus detected in a metagenomic analysis of water sources from the USA, suggesting widespread distribution. RT-PCR analysis revealed that this virus can be detected in a laboratory-grown worm isolate for at least five years, suggesting persistent infection. However, no apparent deleterious effects were observed in the worms in culture, suggesting a possible commensal relationship between the virus and the worms.},
}
@article {pmid39542877,
year = {2024},
author = {Vasudevan, G and Ramachandran, K and Tangavel, C and Nayagam, SM and Gopalakrishnan, C and Muthurajan, R and Sri Vijay Anand, KS and Rajasekaran, S},
title = {"Elucidating the immunomodulatory role of endocannabinoids in intervertebral disc degeneration".},
journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society},
volume = {},
number = {},
pages = {},
pmid = {39542877},
issn = {1432-0932},
abstract = {PURPOSE: The endocannabinoid system (ECS) has been well-established to play a crucial role in the regulation of several physiological processes as well as many inflammatory disease conditions. However, its role in intervertebral disc degeneration has been least explored. We aim to investigate the immunomodulatory role of endocannabinoids in regulating IVD health.<br><br>METHODS: The study population included 20 healthy volunteers (controls) and 40 patients with disc degeneration (disease group) (20 Modic and 20 Non Modic). 16S metagenome sequencing of the V3-V4 region was performed for the DNA extracted from NP tissue samples of both control and disease groups. Sequencing was carried out using the Novaseq 6000 platform using 250&#xa0;bp paired-end chemistry. A global metabolic profile was obtained using the uHPLC system coupled with Q Exactive Plus Hybrid Quadrupole-Orbitrap mass spectrometer.<br><br>RESULTS: Our study revealed a higher prevalence of gram-negative bacteria, particularly opportunistic pathogens like Pseudomonas, in diseased discs (71-81%) compared to healthy controls (54%). Further investigation using metabolomics identified significant changes in the lipid profiles of diseased discs. We found that the signalling molecules of the ECS, 2-arachidonylglycerol (2-AG) and N-arachidonoylethanolamine (AEA), were significantly lower in diseased discs compared to controls (Log2FC -2.62 for 2-AG and &#x2009;-3.15 for AEA). Conversely, pro-inflammatory metabolites like LTA4, HPETE, HETE, and Prostaglandin G2 were elevated in diseased discs, with a Log2 fold increase greater than 2.5.<br><br>CONCLUSION: The study reveals that the endocannabinoid metabolites (2-AG and AEA) of the ECS could be a significant molecule influencing susceptibility to infection and inflammation within the intervertebral discs, which could be a potential target for improving disc health.<br><br>LEVEL OF EVIDENCE: Diagnostic: individual cross-sectional studies with consistently applied reference standard and blinding.},
}
@article {pmid39542187,
year = {2024},
author = {Gurumayum, N and Devi, MB and Khound, P and Bhattacharya, A and Sarma, H and Khan, MR and Devi, R},
title = {Bioactive fraction of Musa balbisiana seed mitigates D-galactose-induced brain aging via SIRT1/PGC-1α/FoxO3a activation and intestinal barrier dysfunction by modulating gut microbiota and core metabolites.},
journal = {Free radical biology &amp; medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.freeradbiomed.2024.11.016},
pmid = {39542187},
issn = {1873-4596},
abstract = {Aging is an inevitable biological process, and emerging research has highlighted the potential of dietary and pharmacological interventions to decelerate the trajectory of age-related diseases and prolong the health span. This study evaluates the protective effects of Musa balbisiana seed on healthy aging using D-galactose-induced accelerated aging rats. The results suggested that the bioactive ethyl acetate fraction of Musa balbisiana seed extract (BF) exhibited protective effects against aging-induced oxidative stress by reducing oxidative DNA damage, advanced glycation end-product formation, and malondialdehyde levels while restoring antioxidant and glyoxalase enzyme activities. BF also ameliorated neurodegeneration by decreasing acetylcholinesterase enzyme activity and amyloid beta plaque formation. Histopathological analysis demonstrated the protective effects of BF against brain aging, liver disruption, renal damage, and intestinal barrier dysfunction. BF further restored intestinal permeability by upregulating the tight junctions (zonula occludens 1 and 2, claudin 1,2,3 and 4, and occludin) and mucin (mucin 2 and mucin 5ac) gene expression while downregulating the expression of inflammatory cytokines (IL-1β, IL-6, and TNF-α). BF significantly induced the phosphorylation of FoxO3a proteins and upregulated the gene expression of SIRT1, PGC-1α, and TFAM in the hippocampus. Next-generation sequencing (NGS) of 16s rRNA amplicons of fecal metagenomics DNA and metabolites profiling showed that BF intervention restructured the gut microbiota and altered core metabolites related to cholesterol metabolism. Overall, our findings demonstrated the multifaceted protective effects of Musa balbisiana seed against D-galactose-induced aging.},
}
@article {pmid39542137,
year = {2024},
author = {Gonzalez, FJ and Xia, Y},
title = {Adipose triglyceride lipase as a target for treatment of metabolic dysfunction-associated steatohepatitis: the role of hepatic and intestinal PPARα.},
journal = {Journal of hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhep.2024.10.046},
pmid = {39542137},
issn = {1600-0641},
}
@article {pmid39542062,
year = {2024},
author = {Wimalaweera, I and Zuo, F and Qihe Tang, and Sui, Q and Jinadasa, S and Weragoda, S and Ritigala, T and Weerasooriya, R and Wang, Y and Zhong, H and Makehelwala, M and Wei, Y},
title = {Synchronised removal of nitrogen and sulphate from rubber industrial wastewater by coupling of Sulfammox and sulphide-driven autotrophic denitrification in anaerobic membrane bioreactor.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131785},
doi = {10.1016/j.biortech.2024.131785},
pmid = {39542062},
issn = {1873-2976},
abstract = {Global rubber industry, growing 4-6 % annually with 13.76 million Mt of rubber produced in 2019, significantly impacts the economy. This study explores coupling sulfate-dependent ammonium oxidation (Sulfammox) and sulfide-driven autotrophic denitrification (SDAD) within an anaerobic membrane bioreactor (AnMBR) to treat high-strength natural rubber wastewater. Over 225 days, the AnMBR system achieved maximal chemical oxygen demand (COD), total nitrogen (TN), ammonium nitrogen (NH4[+]-N), and sulfate sulfur (SO4[2-]-S) removal efficiencies of 58 %, 31 %, 13 %, and 45 %, respectively. TN is predominantly removed through Sulfammox (accounting for 49 % of NH4[+]-N removal), SDAD, and conventional denitrification pathways. Sulfate removal is achieved via Sulfammox (responsible for 43 % of SO4[2-]-S removal), and Dissimilatory sulfate-reducing (DSR) processes (contributing 57 % of SO4[2-]-S removal). Microbial analysis identified Desulfovibrio and Sulfurospirillum as key microbes, while metagenomic analysis highlighted crucial sulfur and nitrogen cycling pathways. The findings support Sulfammox and SDAD as promising eco-friendly strategies for treating ammonia- and sulfate-rich industrial wastewater.},
}
@article {pmid39542060,
year = {2024},
author = {Fu, J and Guo, T and Li, H and Liu, W and Chen, Z and Wang, X and Guo, J},
title = {Amorphous Cu/Fe nanoparticles with tandem intracellular and extracellular electron capacity for enhancing denitrification performance and recovery of co-contaminant suppressed denitrification.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131812},
doi = {10.1016/j.biortech.2024.131812},
pmid = {39542060},
issn = {1873-2976},
abstract = {In this study, a functionally stable insoluble Cu/Fe nanoparticles (Cu/Fe NPs) were synthesized and applied denitrification with different contaminants. The results showed that 50 mg/L Cu/Fe NPs increased NO3[-]-N reduction rate up to 14.3 mg/(L·h) about 3 folds compared with the control system (4.7 mg/(L·h)), and Cu/Fe NPs exhibited excellent restorative effects on NO3[-]-N reduction under the stress of Cd[2+], Nitrovin and Methyl Orange. Meanwhile, electrochemical analyses, enzyme activities, and related genes abundance together showed that pilus, cytochrome c and flavin mononucleotide were electron carriers to tandem extracellular and intracellular, increasing electron flux acting on NO3[-]-N in the respiratory chain. Metagenomic sequencing showed that microbial metabolic activity, electroactive bacteria (EAB) abundance with bi-directional electron transfer and Cu/Fe-compatible bacterial abundance were increased. Furthermore, denitrification performance was maintained by establishing C-EAB-Cu/Fe NPs cycling network. This study provided insights and applications for expanding the use of insoluble mediators in denitrification systems.},
}
@article {pmid39541983,
year = {2024},
author = {Urtecho, G and Moody, T and Huang, Y and Sheth, RU and Richardson, M and Descamps, HC and Kaufman, A and Lekan, O and Zhang, Z and Velez-Cortes, F and Qu, Y and Cohen, L and Ricaurte, D and Gibson, TE and Gerber, GK and Thaiss, CA and Wang, HH},
title = {Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut.},
journal = {Cell systems},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cels.2024.10.007},
pmid = {39541983},
issn = {2405-4720},
abstract = {While fecal microbiota transplantation (FMT) has been shown to be effective in reversing gut dysbiosis, we lack an understanding of the fundamental processes underlying microbial engraftment in the mammalian gut. Here, we explored a murine gut colonization model leveraging natural inter-individual variations in gut microbiomes to elucidate the spatiotemporal dynamics of FMT. We identified a natural "super-donor" consortium that robustly engrafts into diverse recipients and resists reciprocal colonization. Temporal profiling of the gut microbiome showed an ordered succession of rapid engraftment by early colonizers within 72 h, followed by a slower emergence of late colonizers over 15-30 days. Moreover, engraftment was localized to distinct compartments of the gastrointestinal tract in a species-specific manner. Spatial metagenomic characterization suggested engraftment was mediated by simultaneous transfer of spatially co-localizing species from the super-donor consortia. These results offer a mechanism of super-donor colonization by which nutritional niches are expanded in a spatiotemporally dependent manner. A record of this paper's transparent peer review process is included in the supplemental information.},
}
@article {pmid39541968,
year = {2024},
author = {Nishijima, S and Stankevic, E and Aasmets, O and Schmidt, TSB and Nagata, N and Keller, MI and Ferretti, P and Juel, HB and Fullam, A and Robbani, SM and Schudoma, C and Hansen, JK and Holm, LA and Israelsen, M and Schierwagen, R and Torp, N and Telzerow, A and Hercog, R and Kandels, S and Hazenbrink, DHM and Arumugam, M and Bendtsen, F and Brøns, C and Fonvig, CE and Holm, JC and Nielsen, T and Pedersen, JS and Thiele, MS and Trebicka, J and Org, E and Krag, A and Hansen, T and Kuhn, M and Bork, P and , },
title = {Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2024.10.022},
pmid = {39541968},
issn = {1097-4172},
abstract = {The microbiota in individual habitats differ in both relative composition and absolute abundance. While sequencing approaches determine the relative abundances of taxa and genes, they do not provide information on their absolute abundances. Here, we developed a machine-learning approach to predict fecal microbial loads (microbial cells per gram) solely from relative abundance data. Applying our prediction model to a large-scale metagenomic dataset (n = 34,539), we demonstrated that microbial load is the major determinant of gut microbiome variation and is associated with numerous host factors, including age, diet, and medication. We further found that for several diseases, changes in microbial load, rather than the disease condition itself, more strongly explained alterations in patients' gut microbiome. Adjusting for this effect substantially reduced the statistical significance of the majority of disease-associated species. Our analysis reveals that the fecal microbial load is a major confounder in microbiome studies, highlighting its importance for understanding microbiome variation in health and disease.},
}
@article {pmid39541850,
year = {2024},
author = {Wang, Y and Li, H and Ding, K and Zhao, X and Liu, M and Xu, L and Gu, L and Li, J and Li, L and He, Q and Liang, J},
title = {Improved anaerobic digestion of food waste under ammonia stress by side-stream hydrogen domestication.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122770},
doi = {10.1016/j.watres.2024.122770},
pmid = {39541850},
issn = {1879-2448},
abstract = {High ammonia concentration inhibits archaea's activity, causing the accumulation of H2 and acetate, which suppresses methane production in anaerobic digestion (AD). The study aimed to enhance microbial hydrogen metabolism through a side-stream hydrogen domestication (SHD) strategy, which involves applying hydrogen stimulation to a portion of the sludge separately. SHD maintained a stable methane yield of 407.5 mL/g VS at a high total ammonia nitrogen (TAN) concentration of 3.1 g/L. In contrast, the control group gradually decreased and stopped methane production at a TAN concentration of 2.3 g/L. Further analysis using enzyme activity assays, flow cytometry, and metagenomics explored the mechanisms underlying ammonia tolerance of SHD-treated group. SHD reshaped the microbial community, enriching homoacetogens and Methanosaeta-dominated methanogenic archaea. Key metabolic pathways including homoacetogenesis, butyrate degradation, propionate degradation, and methane production were enhanced. The activity of related enzymes also increased. Gene abundance in energy-generating pathways, such as glycolysis, was enhanced, ensuring adequate ATP production. Additionally, the high gene abundance of ion transport systems contributed to regulating proton imbalance and supplementing intracellular K[+]. This study provides important insights and practical guidance for developing novel techniques in the field of anaerobic digestion.},
}
@article {pmid39541849,
year = {2024},
author = {Guo, H and Li, R and Xue, S and Zhangsun, X and Huang, D and Li, Y and Li, N and Su, Y and Zhang, H and Huang, T},
title = {Considerable declines in odor in a drinking water reservoir: Variations of odorous community, precursor enzymes abundance, distribution, and environmental dominant factors.},
journal = {Water research},
volume = {268},
number = {Pt B},
pages = {122767},
doi = {10.1016/j.watres.2024.122767},
pmid = {39541849},
issn = {1879-2448},
abstract = {The presence of 2-methylisoborneol (2-MIB) is acknowledged as a prevalent source of odor-related challenges in drinking water reservoirs. Among the three in situ experiments conducted in drinking water reservoir, the water-lifting aerator with bio-filling system exhibited the most pronounced overall effects. It achieved a remarkable 98.70 % removal of 2-MIB and a 99.30 % reduction in the abundance of the mic gene. Metagenomic sequencing identified key genes including methyl transferase gene (mtf), 2-MIB cyclase gene (mic), cyclic nucleotide-binding protein gene (cnb), underscoring the potential role of Actinobacteria, Cyanobacteria, and Proteobacteria communities in contributing to odor occurrences in the reservoir. Furthermore, the abundance of odorous precursor enzymes in the MVA pathway and MEP/DOXP pathway were inhibited in the systems with bio-filling. Total nitrogen (TN) and nitrate (NO3[-]-N) were identified as pivotal factors influencing the presence of 2-MIB odor-producing microorganisms. Effective management of odor-producing species in reservoir water was closely related to the efficient removal of pollutants. These findings will provide valuable insights for the development of odor removal techniques in reservoirs and offer researchers deeper understanding into the mechanisms underlying odor processes.},
}
@article {pmid39541817,
year = {2024},
author = {Czatzkowska, M and Wolak, I and Harnisz, M and Korzeniewska, E},
title = {Microbial diversity and biosafety judgment of digestates derived from different biogas plants for agricultural applications.},
journal = {Journal of environmental management},
volume = {371},
number = {},
pages = {123329},
doi = {10.1016/j.jenvman.2024.123329},
pmid = {39541817},
issn = {1095-8630},
abstract = {The composition of microbial communities is the key to effective anaerobic digestion (AD). The microbiome driving the AD process has been extensively researched, whereas the influence of specific substrates on the microbiome of digestate remains insufficiently investigated. Digestate has considerable potential for use in soil fertilization and bioremediation, therefore its biological safety should be monitored. Moreover, the knowledge about the composition of microbial communities and their interconnections in digestate should be extended, due to the impact on soil microbiota and its functionality. The aim of this study was a comprehensive assessment of the (1) sanitary quality, (2) core microbiome, and (3) microbial interactions in digestates collected from three full-scale agricultural biogas plants, with particular emphasis on their applicability from the perspective of the resident microbiota. Analyzed samples of digestate were derived from various substrates used for AD, including plant- and animal-based materials, and industrial waste. The study demonstrated that the phyla Bacillota, Bacteroidota, and Cloacimonadota were the most dominant in digestates regardless of the composition of the processed substrates, however, member composition at the genus level differed significantly between samples. In addition, we observed that microbial genera belonging to the less prevalent phyla play an integral role in the forming of microbial community interactions. Dominant microbial taxa with broad metabolic capabilities, potentially improving soil quality and functionality, have been identified. Moreover, we confirmed, that digestate samples were free of analyzed pathogenic bacteria and parasites. The study results indicate that digestate may have an immense fertilizing and bioremediation potential that has not been fully availed of to date.},
}
@article {pmid39541434,
year = {2024},
author = {Shi, L and Zhang, D and Yang, Q and Yang, J and Zhu, H},
title = {Distinction of clinical features and microbiological methods between Chlamydia psittaci and Legionella pneumophila pneumonia confirmed by metagenomic next-generation sequencing.},
journal = {Annals of medicine},
volume = {56},
number = {1},
pages = {2428433},
doi = {10.1080/07853890.2024.2428433},
pmid = {39541434},
issn = {1365-2060},
mesh = {Humans ; Male ; *Chlamydophila psittaci/isolation &amp; purification/genetics ; Female ; Retrospective Studies ; Middle Aged ; *Legionella pneumophila/isolation &amp; purification/genetics ; *Psittacosis/diagnosis/microbiology/drug therapy ; Aged ; *Legionnaires' Disease/diagnosis/microbiology/drug therapy ; *Community-Acquired Infections/microbiology/diagnosis ; *High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Diagnosis, Differential ; Adult ; Prognosis ; },
abstract = {OBJECTIVES: Detection and diagnosis of Chlamydia psittaci (C. psittaci) pneumonia is often overlooked due to conventional methods limitations and similarity to other atypical community acquired pneumonia (CAP). Using mNGS, we aimed to distinguish psittacosis from legionellosis for early C. psittaci pneumonia diagnosis and better prognosis.<br><br>METHODS: Thirty-seven patients diagnosed with atypical CAP were enrolled in this retrospective study, including 14&#x2009;C. psittaci pneumonia and 23 Legionella pneumophila (L. pneumophila) pneumonia. We collected and compared baseline, lab results, radiology imaging, conventional microbiological methods and more importantly, mNGS results of clinical samples, as well as the treatments and prognosis between psittacosis and legionellosis.<br><br>RESULTS: Patients with C. psittaci and L. pneumophila had similar symptoms and were presented with high levels of inflammatory markers. However, patients with C. psittaci pneumonia were more likely to have exposure to birds or parrots [11 (78.6%) vs. 2 (8.7%), p&#x2009;<&#x2009;0.001], had higher proportions of fever and chill (p&#x2009;=&#x2009;0.015 and 0.035), higher levels of hemoglobin and albumin (p&#x2009;=&#x2009;0.002 and 0.018) compared with those with L. pneumophila. Of 14&#x2009;C. psittaci patients, only one had positive IgM antibody, with no positive cultures. Early identification of pathogens by mNGS method contributed to timely antibiotics' adjustment and better outcomes then, yet with similar hospital mortality between two groups [7.1% (1/14) vs. 34.8% (8/23), p&#x2009;=&#x2009;0.112].<br><br>CONCLUSION: Early mNGS detection of atypical pathogens in multiple samples improves on traditional methods, promptly adjust empirical antimicrobial treatment to pathogen-targeted antibiotics, further improve prognosis.},
}
@article {pmid39541261,
year = {2024},
author = {Golob, J and Rao, K and Berinstein, JA and Singh, P and Chey, WD and Owyang, C and Kamada, N and Higgins, PDR and Young, V and Bishu, S and Lee, AA},
title = {Why Symptoms Linger in Quiescent Crohn's Disease: Investigating the Impact of Sulfidogenic Microbes and Sulfur Metabolic Pathways.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izae238},
pmid = {39541261},
issn = {1536-4844},
support = {/CCF/CCF/United States ; DK124567/NH/NIH HHS/United States ; },
abstract = {INTRODUCTION: Even in the absence of inflammation, persistent symptoms in patients with Crohn's disease (CD) are prevalent and worsen quality of life. We previously demonstrated enrichment in sulfidogenic microbes in quiescent Crohn's disease patients with (qCD + S) vs without persistent GI symptoms (qCD-S). Thus, we hypothesized that sulfur metabolic pathways would be enriched in stool while differentially abundant microbes would be associated with important sulfur metabolic pathways in qCD + S.<br><br>METHODS: We performed a multicenter observational study nested within SPARC IBD. Quiescent inflammation was defined by fecal calprotectin level&#x2005;<&#x2005;150 mcg/g. Persistent symptoms were defined by CD-PRO2. Active CD (aCD) and non-IBD diarrhea-predominant irritable bowel syndrome (IBS-D) were included as controls.<br><br>RESULTS: Thirty-nine patients with qCD&#x2005;+&#x2005;S, 274 qCD-S, 21 aCD, and 40 IBS-D underwent paired shotgun metagenomic sequencing and untargeted metabolomic profiling. The fecal metabolome in qCD&#x2005;+&#x2005;S was significantly different relative to qCD-S and IBS-D but not aCD. Patients with qCD&#x2005;+&#x2005;S were enriched in sulfur-containing amino acid pathways, including cysteine and methionine, as well as serine, glycine, and threonine. Glutathione and nicotinate/nicotinamide pathways were also enriched in qCD&#x2005;+&#x2005;S relative to qCD-S, suggestive of mitochondrial dysfunction, a downstream target of H2S signaling. Multi-omic integration demonstrated that enriched microbes in qCD&#x2005;+&#x2005;S were associated with important sulfur metabolic pathways. Bacterial sulfur metabolic genes, including CTH, isfD, sarD, and asrC, were dysregulated in qCD&#x2005;+&#x2005;S. Finally, sulfur metabolites with and without sulfidogenic microbes showed good accuracy in predicting the presence of qCD&#x2005;+&#x2005;S.<br><br>DISCUSSION: Microbial-derived sulfur pathways and downstream mitochondrial function are perturbed in qCD&#x2005;+&#x2005;S, which implicate H2S signaling in the pathogenesis of this condition. Future studies will determine whether targeting H2S pathways results in improved quality of life in qCD&#x2005;+&#x2005;S.},
}
@article {pmid39540836,
year = {2024},
author = {Charles, P and Kumar, S and Girish Kumar, CP and Parameswaran, S and Viswanathan, P and Nachiappa Ganesh, R},
title = {Association of gut microbiota with allograft injury in kidney transplant recipients: a comparative profiling through 16S metagenomics and quantitative PCR.},
journal = {Journal of medical microbiology},
volume = {73},
number = {11},
pages = {},
doi = {10.1099/jmm.0.001934},
pmid = {39540836},
issn = {1473-5644},
mesh = {Humans ; *Kidney Transplantation/adverse effects ; *Gastrointestinal Microbiome ; Male ; *RNA, Ribosomal, 16S/genetics ; Female ; Middle Aged ; *Metagenomics/methods ; Adult ; Prospective Studies ; Longitudinal Studies ; *Graft Rejection/microbiology ; Real-Time Polymerase Chain Reaction/methods ; Bacteria/classification/genetics/isolation &amp; purification ; Feces/microbiology ; Allografts/microbiology ; Transplant Recipients ; },
abstract = {Introduction. The existence of a mutual relationship between gut microbiota and immune homeostasis highlights its importance in the context of kidney transplantation.Gap statement. The translational utility of gut microbiota as a biomarker for allograft injury has not been assessed before.Aim. In this study, we aimed to characterize the gut microbial diversity in kidney transplant recipients and investigate the alterations in the gut microbial composition in association with allograft injury such as histopathological graft rejection and calcineurin inhibitor toxicity. In addition, we compared the gut microbial quantitation using 16S metagenomics and quantitative PCR (qPCR) to assess its translational utility.Methodology. In this prospective longitudinal cohort study, we enrolled 38 kidney transplant recipients and collected serial faecal specimens (n=114), once before the induction therapy, and twice after transplant, during the first and third month. We characterized the gut microbial composition through 16S rRNA sequencing and qPCR from the DNA isolates of the samples. The recipients were clinically followed up for a median of 600 days post-transplant. Histopathological evidence of allograft rejection and calcineurin inhibitor toxicity were used for the correlational analysis with gut microbial diversity.Results. Significant differences in the gut microbial diversity were observed between the pre- and post-transplant samples. Pre-transplant gut microbiota revealed a higher relative abundance of phylum Bacteroidetes in the allograft rejection group, and a higher relative abundance of phylum Firmicutes was observed in the histopathological features of calcineurin inhibitor toxicity (hCNI toxicity) group. We found a high concordance between 16S metagenomics and qPCR outputs for assessing the gut microbial diversity. Furthermore, the receiver operating characteristic curve analysis has also proven that the pre-transplant levels of gut microbial dysbiosis, as a potential predictive biomarker for allograft injury.Conclusion. Our pilot study found a strong statistical association of gut microbial dysbiosis with kidney allograft injury, highlighting the potential of gut microbiota as a predictive biomarker and that qPCR serves as a more reliable and economic tool for assessing dysbiosis paving the way for its translational utility.},
}
@article {pmid39540753,
year = {2024},
author = {Zhang, T and Liu, Y and Guo, X and Zhang, X and Zheng, X and Zhang, M and Bao, Y},
title = {VISTA: A Tool for Fast Taxonomic Assignment of Viral Genome Sequences.},
journal = {Genomics, proteomics &amp; bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1093/gpbjnl/qzae082},
pmid = {39540753},
issn = {2210-3244},
abstract = {The rapid expansion of the number of viral genome sequences in public databases necessitates a scalable, universal, and automated preliminary taxonomic framework for comprehensive virus studies. Here, we introduce VISTA (Virus Sequence-based Taxonomy Assignment), a computational tool that employs a novel pairwise sequence comparison system and an automatic demarcation threshold identification framework for virus taxonomy. Leveraging physio-chemical property sequences, k-mer profiles, and machine learning techniques, VISTA constructs a robust distance-based framework for taxonomic assignment. Functionally similar to PASC (Pairwise Sequence Comparison), a widely used virus assignment tool based on pairwise sequence comparison, VISTA demonstrates superior performance by providing significantly improved separation for taxonomic groups, more objective taxonomic demarcation thresholds, greatly enhanced speed, and a wider application scope. We successfully applied VISTA to 38 virus families, as well as to the class Caudoviricetes. This demonstrates VISTA's scalability, robustness, and ability to automatically and accurately assign taxonomy to both prokaryotic and eukaryotic viruses. Furthermore, the application of VISTA to 679 unclassified prokaryotic virus genomes recovered from metagenomic data identified 46 novel virus families. VISTA is available as both a command line tool and a user-friendly web portal at https://ngdc.cncb.ac.cn/vista.},
}
@article {pmid39540749,
year = {2024},
author = {Pavia, MJ and Garber, AI and Avalle, S and Macedo-Tafur, F and Tello-Espinoza, R and Cadillo-Quiroz, H},
title = {Functional insights of novel Bathyarchaeia reveal metabolic versatility in their role in peatlands of the Peruvian Amazon.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0038724},
doi = {10.1128/spectrum.00387-24},
pmid = {39540749},
issn = {2165-0497},
abstract = {UNLABELLED: The decomposition of soil organic carbon within tropical peatlands is influenced by the functional composition of the microbial community. In this study, building upon our previous work, we recovered a total of 28 metagenome-assembled genomes (MAGs) classified as Bathyarchaeia from the tropical peatlands of the Pastaza-Marañón Foreland Basin (PMFB) in the Amazon. Using phylogenomic analyses, we identified nine genus-level clades to have representatives from the PMFB, with four forming a putative novel family ("Candidatus Paludivitaceae") endemic to peatlands. We focus on the Ca. Paludivitaceae MAGs due to the novelty of this group and the limited understanding of their role within tropical peatlands. Functional analysis of these MAGs reveals that this putative family comprises facultative anaerobes, possessing the genetic potential for oxygen, sulfide, or nitrogen oxidation. This metabolic versatility can be coupled to the fermentation of acetoin, propanol, or proline. The other clades outside Ca. Paludivitaceae are putatively capable of acetogenesis and de novo amino acid biosynthesis and encode a high amount of Fe[3+] transporters. Crucially, the Ca. Paludivitaceae are predicted to be carboxydotrophic, capable of utilizing CO for energy generation or biomass production. Through this metabolism, they could detoxify the environment from CO, a byproduct of methanogenesis, or produce methanogenic substrates like CO2 and H2. Overall, our results show the complex metabolism and various lineages of Bathyarchaeia within tropical peatlands pointing to the need to further evaluate their role in these ecosystems.<br><br>IMPORTANCE: With the expansion of the Candidatus Paludivitaceae family by the assembly of 28 new metagenome assembled genomes, this study provides novel insights into their metabolic diversity and ecological significance in peatland ecosystems. From a comprehensive phylogenic and functional analysis, we have elucidated their putative unique facultative anaerobic capabilities and CO detoxification potential. This research highlights their crucial role in carbon cycling and greenhouse gas regulation. These findings are essential for resolving the microbial processes affecting peat soil stability, offering new perspectives on the ecological roles of previously underexplored and underrepresented archaeal populations.},
}
@article {pmid39540745,
year = {2024},
author = {Huang, Y and Schomer, R and Reyes, MJR and Costa, K and Parales, RE and Whitaker, R and Dawson, SC},
title = {Metagenome-assembled genomes of freshwater Hyphomicrobium sp. G-191 and Methylophilus sp. enriched from Cedar Swamp, Woods Hole, MA.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0060824},
doi = {10.1128/mra.00608-24},
pmid = {39540745},
issn = {2576-098X},
abstract = {Hyphomicrobium are facultative denitrifying anaerobes capable of using one-carbon compounds as a sole carbon source. Hyphomicrobium sp. G-191 was enriched from Cedar Swamp, Woods Hole, Massachusetts, using a selective medium for methanol-utilizing bacteria. We present two draft metagenome-assembled genomes (MAGs) of a Hyphomicrobium and a Methylophilus species.},
}
@article {pmid39540551,
year = {2024},
author = {Vepštaitė-Monstavičė, I and Lukša, J and Strazdaitė-Žielienė, &#x17d; and Serva, S and Servienė, E},
title = {Distinct microbial communities associated with health-relevant wild berries.},
journal = {Environmental microbiology reports},
volume = {16},
number = {6},
pages = {e70048},
doi = {10.1111/1758-2229.70048},
pmid = {39540551},
issn = {1758-2229},
support = {S-PD-22-85//Lithuanian Research Council (LMTLT)/ ; },
mesh = {*Fruit/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; *Microbiota ; Vaccinium vitis-idaea/chemistry/microbiology/genetics ; High-Throughput Nucleotide Sequencing ; Rosa/microbiology ; Phylogeny ; },
abstract = {Lingonberries (Vaccinium vitis-idaea L.), rowanberries (Sorbus aucuparia L.) and rosehips (Rosa canina L.) positively affect human health due to their healing properties, determined by a high content of bioactive compounds. The consumption of unprocessed wild berries is relevant and encouraged, making their in-depth microbiological characterization essential for food safety. This study presents the first high-throughput sequencing analysis of bacterial and fungal communities distributed on the surface of lingonberries, rowanberries and rosehips. Significant plant-defined differences in the taxonomic composition of prokaryotic and eukaryotic microbiota were observed. The bacterial community on rosehips was shown to be prevalent by Enterobacteriaceae, lingonberries by Methylobacteriaceae and rowanberries by Sphingomonadaceae representatives. Among the fungal microbiota, Dothioraceae dominated on rosehips and Exobasidiaceae on lingonberries; meanwhile, rowanberries were inhabited by a similar level of a broad spectrum of fungal families. Cultivable yeast profiling revealed that lingonberries were distinguished by the lowest amount and most distinct yeast populations. Potentially pathogenic to humans or plants, as well as beneficial and relevant biocontrol microorganisms, were identified on tested berries. The combination of metagenomics and a cultivation-based approach highlighted the wild berries-associated microbial communities and contributed to uncovering their potential in plant health, food and human safety.},
}
@article {pmid39540428,
year = {2024},
author = {Paysan-Lafosse, T and Andreeva, A and Blum, M and Chuguransky, SR and Grego, T and Pinto, BL and Salazar, GA and Bileschi, ML and Llinares-López, F and Meng-Papaxanthos, L and Colwell, LJ and Grishin, NV and Schaeffer, RD and Clementel, D and Tosatto, SCE and Sonhammer, E and Wood, V and Bateman, A},
title = {The Pfam protein families database: embracing AI/ML.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae997},
pmid = {39540428},
issn = {1362-4962},
support = {221320/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; BB/X012492/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //European Molecular Biology Laboratory/ ; 823886//European Union's H2020 Marie Sk&#x142;odowska-Curie Actions/ ; //European Union-NextGenerationEU/ ; IR0000010//ElixirxNextGenIT/ ; 2224128//National Science Foundation/ ; },
abstract = {The Pfam protein families database is a comprehensive collection of protein domains and families used for genome annotation and protein structure and function analysis (https://www.ebi.ac.uk/interpro/). This update describes major developments in Pfam since 2020, including decommissioning the Pfam website and integration with InterPro, harmonization with the ECOD structural classification, and expanded curation of metagenomic, microprotein and repeat-containing families. We highlight how AlphaFold structure predictions are being leveraged to refine domain boundaries and identify new domains. New families discovered through large-scale sequence similarity analysis of AlphaFold models are described. We also detail the development of Pfam-N, which uses deep learning to expand family coverage, achieving an 8.8% increase in UniProtKB coverage compared to standard Pfam. We discuss plans for more frequent Pfam releases integrated with InterPro and the potential for artificial intelligence to further assist curation. Despite recent advances, many protein families remain to be classified, and Pfam continues working toward comprehensive coverage of the protein universe.},
}
@article {pmid39539714,
year = {2024},
author = {Hauptmann, AL and Johansen, J and Stæger, FF and Nielsen, DS and Mulvad, G and Hanghøj, K and Rasmussen, S and Hansen, T and Albrechtsen, A},
title = {Gut heavy metal and antibiotic resistome of humans living in the high Arctic.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1493803},
doi = {10.3389/fmicb.2024.1493803},
pmid = {39539714},
issn = {1664-302X},
abstract = {Contaminants, such as heavy metals (HMs), accumulate in the Arctic environment and the food web. The diet of the Indigenous Peoples of North Greenland includes locally sourced foods that are central to their nutritional, cultural, and societal health but these foods also contain high concentrations of heavy metals. While bacteria play an essential role in the metabolism of xenobiotics, there are limited studies on the impact of heavy metals on the human gut microbiome, and it is so far unknown if and how Arctic environmental contaminants impact the gut microbes of humans living in and off the Arctic environment. Using a multiomics approach including amplicon, metagenome, and metatranscriptome sequencing, we identified and assembled a near-complete (NC) genome of a mercury-resistant bacterial strain from the human gut microbiome, which expressed genes known to reduce mercury toxicity. At the overall ecological level studied through α- and β-diversity, there was no significant effect of heavy metals on the gut microbiota. Through the assembly of a high number of NC metagenome-assembled genomes (MAGs) of human gut microbes, we observed an almost complete overlap between heavy metal-resistant strains and antibiotic-resistant strains in which resistance genes were all located on the same genetic elements.},
}
@article {pmid39538984,
year = {2024},
author = {Zhang, Y and Song, Z and Schilling, JS},
title = {Evaluation of DNA Extraction Methods for Microbial Community Profiling in Deadwood Decomposition.},
journal = {MicrobiologyOpen},
volume = {13},
number = {6},
pages = {e70007},
doi = {10.1002/mbo3.70007},
pmid = {39538984},
issn = {2045-8827},
support = {//Funding for the study was provided by a Jr. Faculty grant to J.S.S. from the Andrew W. Mellon Foundation (New York, NY)./ ; },
mesh = {*Wood/microbiology ; *Fungi/genetics/classification/isolation &amp; purification ; *Bacteria/genetics/classification/isolation &amp; purification ; *Betula/microbiology ; *DNA, Fungal/genetics ; *Microbiota/genetics ; Pinus/microbiology ; DNA, Bacterial/genetics ; Metagenomics/methods ; Sequence Analysis, DNA/methods ; },
abstract = {As technologies advance alongside metabarcoding and metagenomic resources, particularly for larger fungal genomes, DNA extraction methods must be optimized to meet higher thresholds, especially from complex environmental substrates. This study focused on extracting fungal genomic compounds from woody substrates, a challenge due to the embedment of endophytic and saprotrophic fungi within wood cells, the physical recalcitrance of wood, the adsorption of nucleic acids to wood polymers, and the release of downstream inhibitors. Hypothesizing that cetyltrimethylammonium bromide would be the best option, we compared prominent methods by extracting and sequencing microbial DNA from sound and decayed birch (Betula papyrifera) and pine (Pinus resinosa). DNA quantities varied significantly depending on extraction methods and decay stage. The quality of DNA, in terms of purity and integrity, significantly impacted whether the samples could be amplified and sequenced. However, amplicon sequencing of bacterial and fungal communities revealed no significant extraction bias. This, along with the sequencing effectiveness and cost/time efficiency, indicates that Qiagen is the gold standard for woody substrates. This study increases confidence in published amplicon data sets regardless of the extraction methods, provides a cost-benefit table for making protocol decisions, and offers guidance on fungal DNA extractions from complex organic substrates (sound and decayed wood) that would best suit future metagenomic efforts.},
}
@article {pmid39538360,
year = {2024},
author = {Malik, M and Chiers, K and Chantziaras, I and Maes, D},
title = {Porcine ear necrosis in nursery piglets is preceded by oral manipulations of the ear.},
journal = {Porcine health management},
volume = {10},
number = {1},
pages = {51},
pmid = {39538360},
issn = {2055-5660},
abstract = {BACKGROUND: Porcine ear necrosis (PEN) is characterized by dry crusts on the ear tip. The crusts often progress to moist and bloody lesions and may lead to partial loss of the ear tissue. The cause and pathophysiology of PEN are unknown. Skin infections, systemic infections, or ear biting have been suggested as a cause of PEN, but no proper evidence has been shown. The behavioural factor has not yet been investigated, therefore this study evaluated the importance of oral manipulations in the occurrence of PEN in nursery pigs. Three farms affected by PEN were visited weekly, and the prevalence and severity were recorded. Video recordings of the animals were performed, and the behaviour was evaluated. The presence of pathogens in the lesions and histological alterations were also analysed.<br><br>RESULTS: The highest percentage of pigs with PEN lesions in the farms ranged between 58 and 93%, with most lesions being of mild to moderate severity. The first ear lesions occurred about 1-2&#xa0;weeks after an increase in the number of ear manipulations in the pens. The frequency of the ear manipulations clearly changed over time, and the number of oral ear manipulation behaviour significantly differed (P&#x2009;<&#x2009;0.05) between pigs in pens with high and low PEN prevalence. Increased ear manipulation behaviour was significantly related to a subsequent increase in PEN lesions (OR&#x2009;=&#x2009;4.3; P&#x2009;<&#x2009;0.001). Metagenomic investigation of lesion scrapings revealed a variety of pathogens mostly with low abundance, where microscopic alterations were found mainly in the epidermis.<br><br>CONCLUSIONS: Oral manipulation of the ear pinnae by pen mates was followed by the development of PEN lesions one to two weeks later. This suggests that the behaviour played an important role in the PEN lesions formation in the nursery pigs of the three farms. Bacteria found in PEN lesions most probably were secondary to initial external skin damage, but their relevance needs to be investigated further.},
}
@article {pmid39538341,
year = {2024},
author = {Pearce, CS and Bukovsky, D and Douchant, K and Katoch, A and Greenlaw, J and Gale, DJ and Nashed, JY and Brien, D and Kuhlmeier, VA and Sabbagh, MA and Blohm, G and De Felice, FG and Pare, M and Cook, DJ and Scott, SH and Munoz, DP and Sjaarda, CP and Tusche, A and Sheth, PM and Winterborn, A and Boehnke, S and Gallivan, JP},
title = {Changes in social environment impact primate gut microbiota composition.},
journal = {Animal microbiome},
volume = {6},
number = {1},
pages = {66},
pmid = {39538341},
issn = {2524-4671},
support = {NFREF-2021-00936//New Frontiers in Research Fund/ ; },
abstract = {BACKGROUND: The gut microbiota (GM) has proven to be essential for both physical health and mental wellbeing, yet the forces that ultimately shape its composition remain opaque. One critical force known to affect the GM is the social environment. Prior work in humans and free-ranging non-human primates has shown that cohabitation and frequent social interaction can lead to changes in GM composition. However, it is difficult to assess the direction of causation in these studies, and interpretations are complicated by the influence of uncontrolled but correlated factors, such as shared diet.<br><br>RESULTS: We performed a 15-month longitudinal investigation wherein we disentangled the impacts of diet and social living conditions on GM composition in a captive cohort of 13 male cynomolgus macaques. The animals were in single housing for the first 3 months of the study initially&#xa0;with a variable diet. After baseline data collection they were placed on a controlled diet for the remainder of the study. Following this diet shift the animals were moved to paired housing for 6 months, enabling enhanced social interaction, and then subsequently returned to single housing at the end of our study. This structured sequencing of diet and housing changes allowed us to assess their distinct impacts on GM composition. We found that the early dietary adjustments led to GM changes in both alpha and beta diversity, whereas changes in social living conditions only altered beta diversity. With respect to the latter, we found that two particular bacterial families - Lactobacillaceae and Clostridiaceae - demonstrated significant shifts in abundance during the transition from single housing to paired housing, which was distinct from the shifts we observed based on a change in diet. Conversely, we found that other bacteria previously associated with sociality were not altered based on changes in social living conditions but rather only by changes in diet.<br><br>CONCLUSIONS: Together, these findings decouple the influences that diet and social living have on GM composition and reconcile previous observations in the human and animal literatures. Moreover, the results indicate biological alterations of the gut that may, in part, mediate the relationship between sociality and wellbeing.},
}
@article {pmid39538316,
year = {2024},
author = {Krasnikov, N and Gulyukin, A and Aliper, T and Yuzhakov, A},
title = {Complete genome characterization by nanopore sequencing of rotaviruses A, B, and C circulating on large-scale pig farms in Russia.},
journal = {Virology journal},
volume = {21},
number = {1},
pages = {289},
pmid = {39538316},
issn = {1743-422X},
support = {FGUG-2022-0018//Federal State Budget Scientific Institution "Federal Scientific Center VIEV", Moscow, Russia./ ; FGUG-2022-0018//Federal State Budget Scientific Institution "Federal Scientific Center VIEV", Moscow, Russia./ ; FGUG-2022-0018//Federal State Budget Scientific Institution "Federal Scientific Center VIEV", Moscow, Russia./ ; FGUG-2022-0018//Federal State Budget Scientific Institution "Federal Scientific Center VIEV", Moscow, Russia./ ; },
mesh = {Animals ; Swine ; *Rotavirus/genetics/classification/isolation &amp; purification ; *Phylogeny ; *Genome, Viral ; *Nanopore Sequencing ; *Genotype ; *Swine Diseases/virology/epidemiology ; *Rotavirus Infections/virology/veterinary/epidemiology ; Russia/epidemiology ; Farms ; Whole Genome Sequencing ; Feces/virology ; RNA, Viral/genetics ; Metagenomics ; },
abstract = {BACKGROUND: Rotaviruses are the major etiological agents of gastroenteritis and diarrheal outbreaks in plenty of mammalian species